tutorials/2. Creating simulations/Creating SED-ML and COMBINE archives from model files.ipynb

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   "source": [
    "# Creating SED-ML and COMBINE archives from model files"
   ]
  },
  {
   "cell_type": "markdown",
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   "source": [
    "To make it easy for investigators to work with a broad range of model formats, modeling frameworks, simulation types, simulation algorithms, and simulation tools, BioSimulators uses the [Simulation Experiment Description Markup Language (SED-ML)](http://sed-ml.org/) and [COMBINE/OMEX archive](https://combinearchive.org/) formats. \n",
    "\n",
    "BioSimulators uses SED-ML to describe simulation experiments. This includes:\n",
    "* Which models to simulate\n",
    "* How to modify models to simulate variants such as alternative initial conditions\n",
    "* What type of simulations to execute (e.g., steady-state, time course)\n",
    "* Which algorithms to use (e.g., CVODE, SSA)\n",
    "* Which observables to record\n",
    "* How to reduce the recorded values of the observables\n",
    "* How to plot the observables\n",
    "* How to export the observables to reports (e.g., CSV, HDF5)\n",
    "\n",
    "BioSimulators uses COMBINE/OMEX archives to bundle the multiple files typically involved in modeling projects into a single archive.\n",
    "* Models (e.g., in CellML, SBML format)\n",
    "* Simulation experiments (SED-ML files)\n",
    "* Visualizations for visualizing simulation results (e.g., in [Vega format](https://vega.github.io/vega/))\n",
    "* Supplementary files, such as data used to calibrate the model\n",
    "* Metadata about the simulation project (RDF files that follow the [OMEX Metadata guidelines](http://co.mbine.org/standards/omex-metadata))\n",
    "\n",
    "This tutorial illustrates how to use the create COMBINE/OMEX archives from model files by illustrating the construction of a COMBINE/OMEX archive for a [flux balance model of the core metabolism of Escherichia coli](../_data/Escherichia-coli-core-metabolism.xml) encoded in SBML."
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   "source": [
    "## 1. Create a SED-ML file and COMBINE archive online"
   ]
  },
  {
   "cell_type": "markdown",
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   "source": [
    "[runBioSimuations](https://run.biosimulations.org/utils/create-project) provides a simple web form for building COMBINE/OMEX archives with SED-ML files from model files (e.g., CellML, SBML). This tool support all of the modeling languages supported by BioSimulators."
   ]
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   "source": [
    "## 2. Create a SED-ML file and COMBINE archive with the command-line program"
   ]
  },
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   "source": [
    "[BioSimulators-utils](https://github.com/biosimulators/Biosimulators_utils) provides a command-line application building COMBINE/OMEX archives with SED-ML files from model files. Like the online program, this tool support all of the modeling languages supported by BioSimulators."
   ]
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   "cell_type": "markdown",
   "id": "1e94699e-0979-4417-a6e2-6410feab0cc4",
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   "source": [
    "First, install [BioSimulators-utils](https://github.com/biosimulators/Biosimulators_utils). Installation instructions are available at [https://docs.biosimulators.org](https://docs.biosimulators.org/Biosimulators_utils). Note, BioSimulators-utils must be installed with the installation options for the model languages that you wish to generate simulations for. A Docker image with BioSimulators utils and all dependencies is also available ([`ghcr.io/biosimulators/biosimulators`](https://github.com/biosimulators/Biosimulators/pkgs/container/biosimulators))."
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   "source": [
    "Inline help for the `biosimulators-utils` command-line program is available by running the program with the `--help` option. Additional help is avilable at [https://docs.biosimulators.org](https://docs.biosimulators.org/Biosimulators_utils/)."
   ]
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     "text": [
      "usage: biosimulators-utils build-project [-h]\n",
      "                                         model-language model-filename\n",
      "                                         simulation-type archive-filename\n",
      "\n",
      "Build a COMBINE/OMEX archive with a SED-ML file for a model\n",
      "\n",
      "positional arguments:\n",
      "  model-language    Model language (`BNGL`, `CellML`, `RBA`, `SBML`,\n",
      "                    `Smoldyn`, or `XPP`)\n",
      "  model-filename    Path to model\n",
      "  simulation-type   Type of simulation (`OneStep`, `SteadyState`, or\n",
      "                    `UniformTimeCourse`)\n",
      "  archive-filename  Path to save archive\n",
      "\n",
      "optional arguments:\n",
      "  -h, --help        show this help message and exit\n"
     ]
    }
   ],
   "source": [
    "!biosimulators-utils build-project --help"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3204a516-2cfb-4749-b752-4d2c9e6a5456",
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   "source": [
    "Next, create a temporary directory to store the created COMBINE/OMEX archive."
   ]
  },
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   "source": [
    "import os\n",
    "if not os.path.isdir('tmp'):\n",
    "    os.mkdir('tmp')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "eca2bf37-9938-4969-9b46-845d457251db",
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   "source": [
    "Next, use the command-line program to build a SED-ML file and COMBINE archive from a [model file](../_data/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.xml)."
   ]
  },
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     "text": [
      "/home/jonrkarr/.local/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\n",
      "  - Model `model` may be invalid.\n",
      "    - The model file `Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.xml` may be invalid.\n",
      "      - The value of the 'sboTerm' attribute on a <species> is expected to be an SBO identifier (http://www.biomodels.net/SBO/). In SBML Level 2 prior to Version 4 it is expected to refer to a participant physical type (i.e., terms derived from SBO:0000236, \"participant physical type\"); in Versions 4 and above it is expected to refer to a material entity (i.e., terms derived from SBO:0000240, \"material entity\").\n",
      "        Reference: L2V4 Section 5\n",
      "         SBO term 'SBO:0000014' on the <species> is not in the appropriate branch.\n",
      "        \n",
      "      - The value of the 'sboTerm' attribute on a <species> is expected to be an SBO identifier (http://www.biomodels.net/SBO/). In SBML Level 2 prior to Version 4 it is expected to refer to a participant physical type (i.e., terms derived from SBO:0000236, \"participant physical type\"); in Versions 4 and above it is expected to refer to a material entity (i.e., terms derived from SBO:0000240, \"material entity\").\n",
      "        Reference: L2V4 Section 5\n",
      "         SBO term 'SBO:0000236' on the <species> is not in the appropriate branch.\n",
      "        \n",
      "      - The value of the 'sboTerm' attribute on a <species> is expected to be an SBO identifier (http://www.biomodels.net/SBO/). In SBML Level 2 prior to Version 4 it is expected to refer to a participant physical type (i.e., terms derived from SBO:0000236, \"participant physical type\"); in Versions 4 and above it is expected to refer to a material entity (i.e., terms derived from SBO:0000240, \"material entity\").\n",
      "        Reference: L2V4 Section 5\n",
      "         SBO term 'SBO:0000236' on the <species> is not in the appropriate branch.\n",
      "        \n",
      "      - The value of the 'sboTerm' attribute on a <parameter> is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, \"quantitative systems description parameter\"). \n",
      "        Reference: L2V4 Sections 4.9.5 and 5\n",
      "         SBO term 'SBO:0000336' on the <parameter> is not in the appropriate branch.\n",
      "        \n",
      "      - The value of the 'sboTerm' attribute on a <parameter> is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, \"quantitative systems description parameter\"). \n",
      "        Reference: L2V4 Sections 4.9.5 and 5\n",
      "         SBO term 'SBO:0000336' on the <parameter> is not in the appropriate branch.\n",
      "        \n",
      "      - The value of the 'sboTerm' attribute on a <parameter> is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, \"quantitative systems description parameter\"). \n",
      "        Reference: L2V4 Sections 4.9.5 and 5\n",
      "         SBO term 'SBO:0000393' on the <parameter> is not in the appropriate branch.\n",
      "        \n",
      "      - The value of the 'sboTerm' attribute on a <parameter> is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, \"quantitative systems description parameter\"). \n",
      "        Reference: L2V4 Sections 4.9.5 and 5\n",
      "         SBO term 'SBO:0000393' on the <parameter> is not in the appropriate branch.\n",
      "        \n",
      "      - The value of the 'sboTerm' attribute on a <parameter> is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, \"quantitative systems description parameter\"). \n",
      "        Reference: L2V4 Sections 4.9.5 and 5\n",
      "         SBO term 'SBO:0000393' on the <parameter> is not in the appropriate branch.\n",
      "        \n",
      "      - The value of the 'sboTerm' attribute on a <parameter> is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, \"quantitative systems description parameter\"). \n",
      "        Reference: L2V4 Sections 4.9.5 and 5\n",
      "         SBO term 'SBO:0000393' on the <parameter> is not in the appropriate branch.\n",
      "        \n",
      "      - The value of the 'sboTerm' attribute on a <parameter> is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, \"quantitative systems description parameter\"). \n",
      "        Reference: L2V4 Sections 4.9.5 and 5\n",
      "         SBO term 'SBO:0000393' on the <parameter> is not in the appropriate branch.\n",
      "        \n",
      "      - The value of the 'sboTerm' attribute on a <parameter> is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, \"quantitative systems description parameter\"). \n",
      "        Reference: L2V4 Sections 4.9.5 and 5\n",
      "         SBO term 'SBO:0000393' on the <parameter> is not in the appropriate branch.\n",
      "        \n",
      "      - The value of the 'sboTerm' attribute on a <parameter> is expected to be an SBO identifier (http://www.biomodels.net/SBO/) referring to a quantitative parameter defined in SBO (i.e., terms derived from SBO:0000002, \"quantitative systems description parameter\"). \n",
      "        Reference: L2V4 Sections 4.9.5 and 5\n",
      "         SBO term 'SBO:0000393' on the <parameter> is not in the appropriate branch.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <assignmentRule> <math> expression 'kswe_prime * Swe1 + kswe_doubleprime * Swe1M + kswe_tripleprime * PSwe1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <assignmentRule> <math> expression 'kmih_prime * Mih_ast + kmih_doubleprime * Mih' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <assignmentRule> <math> expression 'IEtot - IE' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <assignmentRule> <math> expression 'Cdh1tot - Cdh1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <assignmentRule> <math> expression 'Mih1tot - Mih1a' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <assignmentRule> <math> expression 'Mcmtot - Mcm' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <assignmentRule> <math> expression 'SBFtot - SBF' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'kdiss * Trim' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'Trim * (kdsic_prime * Cln + kdsic_doubleprime * Clb + kdsic)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'Trim * (kdclb_doubleprime * Cdh1 + kdclb_tripleprime * Cdc20a + kdclb_prime)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'Trim * kswe' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'kass * Sic * Clb' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'PTrim * kmih' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'Clb * (kdclb_doubleprime * Cdh1 + kdclb_tripleprime * Cdc20a + kdclb_prime)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'kswe * Clb' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'ksclb * mass * Jm * (eps + Mcm) / (mass + Jm)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'kmih * PClb' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'SBF * (kisbf_prime + kisbf_doubleprime * Clb) / (jisbf + SBF)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'SBFin * (kasbf_prime * mass + kasbf_doubleprime * Cln) / (jasbf + SBFin)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'IE * kiie / (jiie + IE)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'kaie * IEin * Clb / (jaie + IEin)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'Cdc20a * kicdc20 / (jicdc20 + Cdc20a)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'kdcdc20 * Cdc20a' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'kacdc20 * Cdc20 * IE / (jacdc20 + Cdc20)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'Cdh1 * (kicdh * Clb + kicdh_prime * Cln) / (jicdh + Cdh1)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'Cdh1in * (Kacdh_prime + Kacdh_doubleprime * Cdc20a) / (jacdh + Cdh1in)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'khsl1 * BUD * Swe1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'khsl1 * BUD * PSwe1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'Viwee * Swe1 * Clb / (Jiwee + Swe1)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'Viwee * Swe1M * Clb / (Jiwee + Swe1M)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'kdswe_prime * Swe1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'khsl1r * Swe1M' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'khsl1r * PSwe1M' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'PSwe1 * Vawee / (Jawee + PSwe1)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'PSwe1M * Vawee / (Jawee + PSwe1M)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'ksswe * SBF' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'kssweC' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'kdswe_prime * PSwe1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'kdiss * PTrim' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'PTrim * (kdclb_doubleprime * Cdh1 + kdclb_tripleprime * Cdc20a + kdclb_prime)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'PTrim * (kdsic_prime * Cln + kdsic_doubleprime * Clb + kdsic)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'kass * PClb * Sic' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'Mih1a * Vimih / (jimih + Mih1a)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'Vamih * Mih1 * Clb / (Jamih + Mih1)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'Mcm * kimcm / (jimcm + Mcm)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'Mcmin * Clb * kamcm / (jamcm + Mcmin)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'kdbud * BE' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'ksbud * Cln' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'Sic * (kdsic_prime * Cln + kdsic_doubleprime * Clb + kdsic)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'kssic' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'kdcln * Cln' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'kscln * SBF' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'kdswe_prime * Swe1M' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'kdcdc20 * Cdc20' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'kscdc20_prime + kscdc20_doubleprime * pow(Clb, 4) / (pow(jscdc20, 4) + pow(Clb, 4))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'kdswe_doubleprime * PSwe1M' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'PClb * (kdclb_doubleprime * Cdh1 + kdclb_tripleprime * Cdc20a + kdclb_prime)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <kineticLaw> <math> expression 'mu * mass' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <event> <trigger> expression 'gt(Clb, 0.2)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <eventAssignment> <math> expression '1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <event> <trigger> expression 'and(lt(Clb, 0.2), gt(flag, 0))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <eventAssignment> <math> expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <eventAssignment> <math> expression '0.5 * mass' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <event> <trigger> expression 'or(geq(Clb, 0.2), geq(BE, 0.6))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <eventAssignment> <math> expression '1' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <event> <trigger> expression 'and(lt(Clb, 0.2), lt(BE, 0.6))' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \n",
      "         The units of the <eventAssignment> <math> expression '0' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kswe' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kswe_prime' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kswe_doubleprime' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kswe_tripleprime' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kmih' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kmih_prime' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'Mih_ast' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kmih_doubleprime' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'Mih' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'IEin' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'IEtot' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'Cdh1in' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'Cdh1tot' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'Mih1' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'Mih1tot' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'Mcmin' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'Mcmtot' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'SBFin' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'SBFtot' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kdiss' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kdsic_prime' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kdsic_doubleprime' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kdsic' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kdclb_doubleprime' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kdclb_tripleprime' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kdclb_prime' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kass' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'ksclb' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'Jm' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'eps' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kisbf_prime' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kisbf_doubleprime' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'jisbf' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kasbf_prime' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kasbf_doubleprime' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'jasbf' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kiie' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'jiie' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kaie' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'jaie' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kicdc20' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'jicdc20' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kdcdc20' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kacdc20' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'jacdc20' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kicdh' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kicdh_prime' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'jicdh' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'Kacdh_prime' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'Kacdh_doubleprime' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'jacdh' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'khsl1' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'BUD' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'Viwee' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'Jiwee' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kdswe_prime' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'khsl1r' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'Vawee' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'Jawee' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'ksswe' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kssweC' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'Vimih' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'jimih' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'Vamih' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'Jamih' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kimcm' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'jimcm' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kamcm' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'jamcm' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kdbud' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'ksbud' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kssic' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kdcln' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kscln' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kscdc20_prime' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kscdc20_doubleprime' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'jscdc20' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'kdswe_doubleprime' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'mu' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'flag' does not have a 'units' attribute.\n",
      "        \n",
      "      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\n",
      "         The <parameter> with the id 'Swe1T' does not have a 'units' attribute.\n",
      "        \n",
      "    - The changes of the model may be invalid.\n",
      "      - Change `init_conc_species_Trim` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `init_conc_species_Clb` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `init_conc_species_Sic` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `init_conc_species_PTrim` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `init_conc_species_PClb` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `init_conc_species_SBF` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `init_conc_species_IE` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `init_conc_species_Cdc20a` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `init_conc_species_Cdc20` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `init_conc_species_Cdh1` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `init_conc_species_Swe1` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `init_conc_species_Swe1M` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `init_conc_species_PSwe1` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `init_conc_species_PSwe1M` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `init_conc_species_Mih1a` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `init_conc_species_Mcm` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `init_conc_species_BE` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `init_conc_species_Cln` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `init_conc_species_mass` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `init_size_compartment_compartment` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kswe_prime` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kswe_doubleprime` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kswe_tripleprime` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kmih_prime` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_Mih_ast` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kmih_doubleprime` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_Mih` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_IEtot` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_Cdh1tot` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_Mih1tot` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_Mcmtot` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_SBFtot` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kdiss` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kdsic_prime` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kdsic_doubleprime` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kdsic` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kdclb_doubleprime` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kdclb_tripleprime` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kdclb_prime` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kass` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_ksclb` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_Jm` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_eps` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kisbf_prime` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kisbf_doubleprime` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_jisbf` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kasbf_prime` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kasbf_doubleprime` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_jasbf` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kiie` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_jiie` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kaie` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_jaie` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kicdc20` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_jicdc20` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kdcdc20` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kacdc20` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_jacdc20` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kicdh` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kicdh_prime` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_jicdh` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_Kacdh_prime` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_Kacdh_doubleprime` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_jacdh` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_khsl1` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_BUD` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_Viwee` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_Jiwee` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kdswe_prime` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_khsl1r` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_Vawee` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_Jawee` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_ksswe` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kssweC` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_Vimih` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_jimih` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_Vamih` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_Jamih` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kimcm` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_jimcm` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kamcm` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_jamcm` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kdbud` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_ksbud` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kssic` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kdcln` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kscln` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kscdc20_prime` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kscdc20_doubleprime` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_jscdc20` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_kdswe_doubleprime` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_mu` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `value_parameter_flag` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "  - Data generator `data_generator_dynamics_species_Trim` may be invalid.\n",
      "    - Variable `dynamics_species_Trim` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_dynamics_species_Clb` may be invalid.\n",
      "    - Variable `dynamics_species_Clb` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_dynamics_species_Sic` may be invalid.\n",
      "    - Variable `dynamics_species_Sic` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_dynamics_species_PTrim` may be invalid.\n",
      "    - Variable `dynamics_species_PTrim` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_dynamics_species_PClb` may be invalid.\n",
      "    - Variable `dynamics_species_PClb` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_dynamics_species_SBF` may be invalid.\n",
      "    - Variable `dynamics_species_SBF` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_dynamics_species_IE` may be invalid.\n",
      "    - Variable `dynamics_species_IE` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_dynamics_species_Cdc20a` may be invalid.\n",
      "    - Variable `dynamics_species_Cdc20a` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_dynamics_species_Cdc20` may be invalid.\n",
      "    - Variable `dynamics_species_Cdc20` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_dynamics_species_Cdh1` may be invalid.\n",
      "    - Variable `dynamics_species_Cdh1` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_dynamics_species_Swe1` may be invalid.\n",
      "    - Variable `dynamics_species_Swe1` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_dynamics_species_Swe1M` may be invalid.\n",
      "    - Variable `dynamics_species_Swe1M` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_dynamics_species_PSwe1` may be invalid.\n",
      "    - Variable `dynamics_species_PSwe1` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_dynamics_species_PSwe1M` may be invalid.\n",
      "    - Variable `dynamics_species_PSwe1M` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_dynamics_species_Mih1a` may be invalid.\n",
      "    - Variable `dynamics_species_Mih1a` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_dynamics_species_Mcm` may be invalid.\n",
      "    - Variable `dynamics_species_Mcm` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_dynamics_species_BE` may be invalid.\n",
      "    - Variable `dynamics_species_BE` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_dynamics_species_Cln` may be invalid.\n",
      "    - Variable `dynamics_species_Cln` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_dynamics_species_mass` may be invalid.\n",
      "    - Variable `dynamics_species_mass` may be invalid.\n",
      "      - XPath could not be validated.\u001b[0m\n",
      "  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n"
     ]
    }
   ],
   "source": [
    "!biosimulators-utils build-project \\\n",
    "    SBML \\\n",
    "    ../_data/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.xml \\\n",
    "    UniformTimeCourse \\\n",
    "    tmp/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "856daded-80e8-40e0-9d30-bc3248991b42",
   "metadata": {},
   "source": [
    "## 3. Create a SED-ML file and COMBINE archive programmatically with Python"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fccef785-a3e4-410e-8fb3-dd82d23b2aaf",
   "metadata": {},
   "source": [
    "These online tools are easy to use. However, they provide investigators little flexibility to customize the generation of COMBINE/OMEX archives and SED-ML files, such as to bundle simulations of multiple model files into a single COMBINE/OMEX archive. The BioSimulators-utils Python API provides additional flexibility to customize the creation of COMBINE/OMEX archives."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fe517e8d-33ad-4ace-b028-91d90cf3a2c6",
   "metadata": {
    "tags": []
   },
   "source": [
    "### 3.1. Use `get_parameters_variables_outputs_for_simulation` to introspect the model file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "3fca90b6-e753-4a46-b5c9-03dcd6ee2c0a",
   "metadata": {},
   "outputs": [],
   "source": [
    "from biosimulators_utils.sedml.data_model import ModelLanguage, SteadyStateSimulation\n",
    "from biosimulators_utils.sedml.model_utils import get_parameters_variables_outputs_for_simulation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "2ee776ba-701c-4a27-8144-077b2156af78",
   "metadata": {},
   "outputs": [],
   "source": [
    "model_filename = '../_data/Escherichia-coli-core-metabolism.xml'\n",
    "model_language = ModelLanguage.SBML\n",
    "simulation_type = SteadyStateSimulation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "f728f296-cf22-4042-8717-ff2bb2e7eae4",
   "metadata": {},
   "outputs": [],
   "source": [
    "params, simulations, vars, outputs = get_parameters_variables_outputs_for_simulation(\n",
    "    model_filename, model_language, simulation_type, native_ids=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6b1c90b2-c7af-4915-b8e7-c73298df628d",
   "metadata": {},
   "source": [
    "### 3.2. Sort the outputs to the model into objectives and reaction fluxes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "caf89705-4503-4fcf-b867-b4893ade8514",
   "metadata": {},
   "outputs": [],
   "source": [
    "obj_variables = list(filter(lambda var: var.target.startswith('/sbml:sbml/sbml:model/fbc:listOfObjectives/'), vars))\n",
    "rxn_flux_variables = list(filter(lambda var: var.target.startswith('/sbml:sbml/sbml:model/sbml:listOfReactions/'), vars))"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "94194bcc-3063-482a-aa42-d2266e010e14",
   "metadata": {},
   "source": [
    "### 3.3 Initialize a SED-ML document which describes a flux balance analysis simulation of the model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "8d56dc26-32eb-4e28-b412-4f927f11c9b8",
   "metadata": {},
   "outputs": [],
   "source": [
    "from biosimulators_utils.sedml.data_model import SedDocument, Model, Task, Report\n",
    "import os.path"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "5dcc7ffa-ca46-45eb-b24e-ef3c61d02c7f",
   "metadata": {},
   "outputs": [],
   "source": [
    "# initialize SED document\n",
    "sed_doc = SedDocument()\n",
    "\n",
    "# create model\n",
    "model = Model(\n",
    "    id='model',\n",
    "    source=os.path.basename(model_filename),\n",
    "    language=ModelLanguage.SBML.value,\n",
    "    changes=params,\n",
    ")\n",
    "sed_doc.models.append(model)\n",
    "\n",
    "# attach simulations\n",
    "sed_doc.simulations = simulations\n",
    "\n",
    "# create task\n",
    "task = Task(\n",
    "    id='task',\n",
    "    model=model,\n",
    "    simulation=simulations[0],\n",
    ")\n",
    "sed_doc.tasks.append(task)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0f1ab38e-4729-4812-90d8-c2cb0a07e1dc",
   "metadata": {},
   "source": [
    "### 3.4. Add reports to the model to export the objective and reaction fluxes predicted by the simulation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "7e86a03c-354e-4490-b7f5-2581d2b2eba5",
   "metadata": {},
   "outputs": [],
   "source": [
    "from biosimulators_utils.sedml.data_model import Report, DataSet, DataGenerator"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "6908177c-cb83-45a8-bdf1-3a867422fc93",
   "metadata": {},
   "outputs": [],
   "source": [
    "report = Report(\n",
    "    id='objective',\n",
    "    name='Objective',\n",
    ")\n",
    "sed_doc.outputs.append(report)\n",
    "for var in obj_variables:\n",
    "    var_id = var.id\n",
    "    var_name = var.name\n",
    "\n",
    "    var.id = 'variable_' + var_id\n",
    "    var.name = None\n",
    "\n",
    "    var.task = task\n",
    "    data_gen = DataGenerator(\n",
    "        id='data_generator_{}'.format(var_id),\n",
    "        variables=[var],\n",
    "        math=var.id,\n",
    "    )\n",
    "    sed_doc.data_generators.append(data_gen)\n",
    "    report.data_sets.append(DataSet(\n",
    "        id=var_id,\n",
    "        label=var_id,\n",
    "        name=var_name,\n",
    "        data_generator=data_gen,\n",
    "    ))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "3fdfc652-b711-4ab6-93b4-0a210f703913",
   "metadata": {},
   "outputs": [],
   "source": [
    "report = Report(\n",
    "    id='reaction_fluxes',\n",
    "    name='Reaction fluxes',\n",
    ")\n",
    "sed_doc.outputs.append(report)\n",
    "for var in rxn_flux_variables:\n",
    "    var_id = var.id\n",
    "    var_name = var.name\n",
    "\n",
    "    var.id = 'variable_' + var_id\n",
    "    var.name = None\n",
    "\n",
    "    var.task = task\n",
    "    data_gen = DataGenerator(\n",
    "        id='data_generator_{}'.format(var_id),\n",
    "        variables=[var],\n",
    "        math=var.id,\n",
    "    )\n",
    "    sed_doc.data_generators.append(data_gen)\n",
    "    report.data_sets.append(DataSet(\n",
    "        id=var_id,\n",
    "        label=var_id,\n",
    "        name=var_name if len(rxn_flux_variables) < 4000 else None,\n",
    "        data_generator=data_gen,\n",
    "    ))"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5486ae23-14e3-4600-9d8e-a6d2785a9e8b",
   "metadata": {},
   "source": [
    "### 3.5. Create a temporary directory to collect the files for the COMBINE archive"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "6d2f3101-7449-462e-9afd-617ab11f5bf8",
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import tempfile\n",
    "if not os.path.isdir('tmp'):\n",
    "    os.mkdir('tmp')\n",
    "archive_dirname = tempfile.mkdtemp(dir='tmp/')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "dd823e6b-c661-498a-9060-8efac4a4f7e1",
   "metadata": {},
   "source": [
    "### 3.6. Copy the model file to the temporary directory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "fa74c5cd-fe7a-4ba9-b71f-3684b0a0e572",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'tmp/tmpdvzzdcf3/Escherichia-coli-core-metabolism.xml'"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import shutil\n",
    "shutil.copyfile(model_filename, os.path.join(archive_dirname, os.path.basename(model_filename)))"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6bfba96d-f86c-4d97-a4d2-433c6831e5c2",
   "metadata": {
    "tags": []
   },
   "source": [
    "### 3.7. Export the SED document to a file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "e9d4d701-5a82-495f-864d-bfb05245ff6c",
   "metadata": {},
   "outputs": [],
   "source": [
    "from biosimulators_utils.sedml.io import SedmlSimulationWriter"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "ca71a588-4f5a-41b4-b828-6397c3797b86",
   "metadata": {
    "scrolled": true,
    "tags": []
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/jonrkarr/Documents/Biosimulators_utils/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\n",
      "  - Model `model` may be invalid.\n",
      "    - The model file `Escherichia-coli-core-metabolism.xml` may be invalid.\n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <compartment> 'c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\n",
      "        Reference: L3V1 Section 4.5\n",
      "         The <compartment> 'c' has no discernable units.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <compartment> 'e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\n",
      "        Reference: L3V1 Section 4.5\n",
      "         The <compartment> 'e' has no discernable units.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_13dpg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_13dpg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_2pg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_2pg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_3pg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_3pg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_6pgc_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_6pgc_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_6pgl_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_6pgl_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_ac_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_ac_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_ac_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_ac_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_acald_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_acald_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_acald_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_acald_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_accoa_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_accoa_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_acon_C_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_acon_C_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_actp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_actp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_adp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_adp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_akg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_akg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_akg_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_akg_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_amp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_amp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_atp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_atp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_cit_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_cit_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_co2_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_co2_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_co2_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_co2_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_coa_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_coa_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_dhap_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_dhap_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_e4p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_e4p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_etoh_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_etoh_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_etoh_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_etoh_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_f6p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_f6p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_fdp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_fdp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_for_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_for_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_for_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_for_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_fru_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_fru_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_fum_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_fum_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_fum_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_fum_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_g3p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_g3p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_g6p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_g6p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_glc__D_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_glc__D_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_gln__L_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_gln__L_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_gln__L_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_gln__L_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_glu__L_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_glu__L_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_glu__L_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_glu__L_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_glx_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_glx_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_h2o_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_h2o_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_h2o_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_h2o_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_h_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_h_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_h_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_h_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_icit_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_icit_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_lac__D_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_lac__D_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_lac__D_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_lac__D_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_mal__L_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_mal__L_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_mal__L_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_mal__L_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_nad_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_nad_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_nadh_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_nadh_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_nadp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_nadp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_nadph_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_nadph_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_nh4_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_nh4_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_nh4_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_nh4_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_o2_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_o2_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_o2_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_o2_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_oaa_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_oaa_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_pep_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_pep_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_pi_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_pi_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_pi_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_pi_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_pyr_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_pyr_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_pyr_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_pyr_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_q8_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_q8_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_q8h2_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_q8h2_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_r5p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_r5p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_ru5p__D_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_ru5p__D_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_s7p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_s7p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_succ_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_succ_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_succ_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_succ_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_succoa_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_succoa_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_xu5p__D_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_xu5p__D_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_13dpg_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_2pg_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_3pg_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_6pgc_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_6pgl_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_ac_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_ac_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_acald_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_acald_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_accoa_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_acon_C_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_actp_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_adp_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_akg_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_akg_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_amp_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_atp_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_cit_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_co2_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_co2_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_coa_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_dhap_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_e4p_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_etoh_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_etoh_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_f6p_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_fdp_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_for_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_for_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_fru_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_fum_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_fum_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_g3p_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_g6p_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_glc__D_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_gln__L_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_gln__L_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_glu__L_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_glu__L_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_glx_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_h2o_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_h2o_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_h_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_h_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_icit_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_lac__D_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_lac__D_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_mal__L_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_mal__L_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_nad_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_nadh_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_nadp_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_nadph_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_nh4_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_nh4_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_o2_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_o2_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_oaa_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_pep_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_pi_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_pi_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_pyr_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_pyr_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_q8_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_q8h2_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_r5p_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_ru5p__D_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_s7p_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_succ_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_succ_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_succoa_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_xu5p__D_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "    - The changes of the model may be invalid.\n",
      "      - Change `cobra_default_lb` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `cobra_default_ub` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `cobra_0_bound` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `R_ATPM_lower_bound` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change `R_EX_glc__D_e_lower_bound` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "  - Data generator `data_generator_obj` may be invalid.\n",
      "    - Variable `variable_obj` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ACALD` may be invalid.\n",
      "    - Variable `variable_R_ACALD` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ACALDt` may be invalid.\n",
      "    - Variable `variable_R_ACALDt` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ACKr` may be invalid.\n",
      "    - Variable `variable_R_ACKr` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ACONTa` may be invalid.\n",
      "    - Variable `variable_R_ACONTa` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ACONTb` may be invalid.\n",
      "    - Variable `variable_R_ACONTb` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ACt2r` may be invalid.\n",
      "    - Variable `variable_R_ACt2r` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ADK1` may be invalid.\n",
      "    - Variable `variable_R_ADK1` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_AKGDH` may be invalid.\n",
      "    - Variable `variable_R_AKGDH` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_AKGt2r` may be invalid.\n",
      "    - Variable `variable_R_AKGt2r` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ALCD2x` may be invalid.\n",
      "    - Variable `variable_R_ALCD2x` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ATPM` may be invalid.\n",
      "    - Variable `variable_R_ATPM` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ATPS4r` may be invalid.\n",
      "    - Variable `variable_R_ATPS4r` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_Biomass_Ecoli_core` may be invalid.\n",
      "    - Variable `variable_R_Biomass_Ecoli_core` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_CO2t` may be invalid.\n",
      "    - Variable `variable_R_CO2t` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_CS` may be invalid.\n",
      "    - Variable `variable_R_CS` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_CYTBD` may be invalid.\n",
      "    - Variable `variable_R_CYTBD` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_D_LACt2` may be invalid.\n",
      "    - Variable `variable_R_D_LACt2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ENO` may be invalid.\n",
      "    - Variable `variable_R_ENO` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ETOHt2r` may be invalid.\n",
      "    - Variable `variable_R_ETOHt2r` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_ac_e` may be invalid.\n",
      "    - Variable `variable_R_EX_ac_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_acald_e` may be invalid.\n",
      "    - Variable `variable_R_EX_acald_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_akg_e` may be invalid.\n",
      "    - Variable `variable_R_EX_akg_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_co2_e` may be invalid.\n",
      "    - Variable `variable_R_EX_co2_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_etoh_e` may be invalid.\n",
      "    - Variable `variable_R_EX_etoh_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_for_e` may be invalid.\n",
      "    - Variable `variable_R_EX_for_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_fru_e` may be invalid.\n",
      "    - Variable `variable_R_EX_fru_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_fum_e` may be invalid.\n",
      "    - Variable `variable_R_EX_fum_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_glc__D_e` may be invalid.\n",
      "    - Variable `variable_R_EX_glc__D_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_gln__L_e` may be invalid.\n",
      "    - Variable `variable_R_EX_gln__L_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_glu__L_e` may be invalid.\n",
      "    - Variable `variable_R_EX_glu__L_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_h_e` may be invalid.\n",
      "    - Variable `variable_R_EX_h_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_h2o_e` may be invalid.\n",
      "    - Variable `variable_R_EX_h2o_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_lac__D_e` may be invalid.\n",
      "    - Variable `variable_R_EX_lac__D_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_mal__L_e` may be invalid.\n",
      "    - Variable `variable_R_EX_mal__L_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_nh4_e` may be invalid.\n",
      "    - Variable `variable_R_EX_nh4_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_o2_e` may be invalid.\n",
      "    - Variable `variable_R_EX_o2_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_pi_e` may be invalid.\n",
      "    - Variable `variable_R_EX_pi_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_pyr_e` may be invalid.\n",
      "    - Variable `variable_R_EX_pyr_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_succ_e` may be invalid.\n",
      "    - Variable `variable_R_EX_succ_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FBA` may be invalid.\n",
      "    - Variable `variable_R_FBA` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FBP` may be invalid.\n",
      "    - Variable `variable_R_FBP` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FORt2` may be invalid.\n",
      "    - Variable `variable_R_FORt2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FORti` may be invalid.\n",
      "    - Variable `variable_R_FORti` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FRD7` may be invalid.\n",
      "    - Variable `variable_R_FRD7` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FRUpts2` may be invalid.\n",
      "    - Variable `variable_R_FRUpts2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FUM` may be invalid.\n",
      "    - Variable `variable_R_FUM` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FUMt2_2` may be invalid.\n",
      "    - Variable `variable_R_FUMt2_2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_G6PDH2r` may be invalid.\n",
      "    - Variable `variable_R_G6PDH2r` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GAPD` may be invalid.\n",
      "    - Variable `variable_R_GAPD` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GLCpts` may be invalid.\n",
      "    - Variable `variable_R_GLCpts` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GLNS` may be invalid.\n",
      "    - Variable `variable_R_GLNS` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GLNabc` may be invalid.\n",
      "    - Variable `variable_R_GLNabc` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GLUDy` may be invalid.\n",
      "    - Variable `variable_R_GLUDy` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GLUN` may be invalid.\n",
      "    - Variable `variable_R_GLUN` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GLUSy` may be invalid.\n",
      "    - Variable `variable_R_GLUSy` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GLUt2r` may be invalid.\n",
      "    - Variable `variable_R_GLUt2r` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GND` may be invalid.\n",
      "    - Variable `variable_R_GND` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_H2Ot` may be invalid.\n",
      "    - Variable `variable_R_H2Ot` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ICDHyr` may be invalid.\n",
      "    - Variable `variable_R_ICDHyr` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ICL` may be invalid.\n",
      "    - Variable `variable_R_ICL` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_LDH_D` may be invalid.\n",
      "    - Variable `variable_R_LDH_D` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_MALS` may be invalid.\n",
      "    - Variable `variable_R_MALS` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_MALt2_2` may be invalid.\n",
      "    - Variable `variable_R_MALt2_2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_MDH` may be invalid.\n",
      "    - Variable `variable_R_MDH` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ME1` may be invalid.\n",
      "    - Variable `variable_R_ME1` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ME2` may be invalid.\n",
      "    - Variable `variable_R_ME2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_NADH16` may be invalid.\n",
      "    - Variable `variable_R_NADH16` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_NADTRHD` may be invalid.\n",
      "    - Variable `variable_R_NADTRHD` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_NH4t` may be invalid.\n",
      "    - Variable `variable_R_NH4t` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_O2t` may be invalid.\n",
      "    - Variable `variable_R_O2t` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PDH` may be invalid.\n",
      "    - Variable `variable_R_PDH` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PFK` may be invalid.\n",
      "    - Variable `variable_R_PFK` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PFL` may be invalid.\n",
      "    - Variable `variable_R_PFL` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PGI` may be invalid.\n",
      "    - Variable `variable_R_PGI` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PGK` may be invalid.\n",
      "    - Variable `variable_R_PGK` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PGL` may be invalid.\n",
      "    - Variable `variable_R_PGL` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PGM` may be invalid.\n",
      "    - Variable `variable_R_PGM` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PIt2r` may be invalid.\n",
      "    - Variable `variable_R_PIt2r` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PPC` may be invalid.\n",
      "    - Variable `variable_R_PPC` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PPCK` may be invalid.\n",
      "    - Variable `variable_R_PPCK` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PPS` may be invalid.\n",
      "    - Variable `variable_R_PPS` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PTAr` may be invalid.\n",
      "    - Variable `variable_R_PTAr` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PYK` may be invalid.\n",
      "    - Variable `variable_R_PYK` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PYRt2` may be invalid.\n",
      "    - Variable `variable_R_PYRt2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_RPE` may be invalid.\n",
      "    - Variable `variable_R_RPE` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_RPI` may be invalid.\n",
      "    - Variable `variable_R_RPI` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_SUCCt2_2` may be invalid.\n",
      "    - Variable `variable_R_SUCCt2_2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_SUCCt3` may be invalid.\n",
      "    - Variable `variable_R_SUCCt3` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_SUCDi` may be invalid.\n",
      "    - Variable `variable_R_SUCDi` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_SUCOAS` may be invalid.\n",
      "    - Variable `variable_R_SUCOAS` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_TALA` may be invalid.\n",
      "    - Variable `variable_R_TALA` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_THD2` may be invalid.\n",
      "    - Variable `variable_R_THD2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_TKT1` may be invalid.\n",
      "    - Variable `variable_R_TKT1` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_TKT2` may be invalid.\n",
      "    - Variable `variable_R_TKT2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_TPI` may be invalid.\n",
      "    - Variable `variable_R_TPI` may be invalid.\n",
      "      - XPath could not be validated.\u001b[0m\n",
      "  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n"
     ]
    }
   ],
   "source": [
    "sedml_filename = os.path.join(archive_dirname, 'simulation.sedml')\n",
    "SedmlSimulationWriter().run(sed_doc, sedml_filename)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "09412765-dfe6-413f-8440-6783ccfe9229",
   "metadata": {},
   "source": [
    "### 3.8. Collect metadata about the model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "f8e8fc8b-83c4-4fce-90f4-7a0cf921d99a",
   "metadata": {},
   "outputs": [],
   "source": [
    "import datetime"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "41cc3c58-9418-4796-bb2d-a499c48b31a5",
   "metadata": {
    "scrolled": true,
    "tags": []
   },
   "outputs": [],
   "source": [
    "citation_doi = '10.1186/1752-0509-7-74'\n",
    "now = datetime.datetime.now()\n",
    "metadata = {\n",
    "    \"combine_archive_uri\": 'http://omex-library.org/Escherichia-coli-core-metabolism.omex',\n",
    "    \"uri\": '.',\n",
    "    'title': 'Escherichia coli core metabolism',\n",
    "    'abstract': 'Flux balance analysis model of the metabolism of Escherichia coli',\n",
    "    'keywords': [\n",
    "        'metabolism',\n",
    "        'BiGG',\n",
    "    ],\n",
    "    'description': None,\n",
    "    'taxa': [\n",
    "        {\n",
    "            'uri': 'http://identifiers.org/taxonomy:83333',\n",
    "            'label': 'Escherichia coli K-12',\n",
    "        },\n",
    "    ],\n",
    "    'encodes': [\n",
    "        {\n",
    "            'uri': 'http://identifiers.org/GO:0008152',\n",
    "            'label': 'metabolic process',\n",
    "        },\n",
    "    ],\n",
    "    'thumbnails': [\n",
    "        ''\n",
    "    ],\n",
    "    'sources': [],\n",
    "    'predecessors': [],\n",
    "    'successors': [],\n",
    "    'see_also': [],\n",
    "    'creators': [{\n",
    "        'uri': 'https://identifiers.org/github:opencobra/cobrapy',\n",
    "        'label': 'COBRApy Team',\n",
    "    }],\n",
    "    'contributors': [{\n",
    "        'uri': 'https://identifiers.org/orcid:0000-0002-2605-5080',\n",
    "        'label': 'Jonathan Karr',\n",
    "    }],\n",
    "    'identifiers': [\n",
    "        {\n",
    "            'uri': 'http://identifiers.org/bigg.model:e_coli_core',\n",
    "            'label': 'bigg.model:e_coli_core',\n",
    "        },\n",
    "    ],\n",
    "    'citations': [\n",
    "        {\n",
    "            'uri': 'http://identifiers.org/doi:' + citation_doi,\n",
    "            'label': None,\n",
    "        },\n",
    "    ],\n",
    "    'license': {\n",
    "        'uri': 'http://bigg.ucsd.edu/license',\n",
    "        'label': 'BiGG',\n",
    "    },\n",
    "    'funders': [],\n",
    "    'created': '{}-{:02d}-{:02d}'.format(now.year, now.month, now.day),\n",
    "    'modified': [\n",
    "        '{}-{:02d}-{:02d}'.format(now.year, now.month, now.day),\n",
    "    ],\n",
    "    'other': [],\n",
    "}"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "95cf342a-ae82-4882-b4d9-39c7101ab28f",
   "metadata": {},
   "source": [
    "### 3.9. Use `get_reference` to lookup citation information for the refernece"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "32e708d3-aba5-48ad-92fc-deaa77a0d8ce",
   "metadata": {},
   "outputs": [],
   "source": [
    "from biosimulators_utils.ref.utils import get_reference\n",
    "import Bio.Entrez\n",
    "Bio.Entrez.email = 'john.doe@university.edu'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "0c280568-13b0-4911-9652-327422a589da",
   "metadata": {},
   "outputs": [],
   "source": [
    "citation = get_reference(doi=citation_doi)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b0e7b44c-cefd-4233-bf9d-8cca4e7f0f92",
   "metadata": {},
   "source": [
    "### 3.10. Add the citation to the metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "eccb2dd7-ba7f-4ee6-92ca-e130f41751ab",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "metadata['citations'][0]['label'] = citation.get_citation()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b6ec5521-ac96-424f-a58d-e2a033169c00",
   "metadata": {},
   "source": [
    "### 3.11. Use `get_pubmed_central_open_access_graphics` to retrieve thumbnail images for the model from the [open-access subset of PubMed Central](https://www.ncbi.nlm.nih.gov/pmc/tools/openftlist/)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "7b0e0bd4-8183-4a8b-bab8-6b119e18896b",
   "metadata": {},
   "outputs": [],
   "source": [
    "from biosimulators_utils.ref.utils import get_pubmed_central_open_access_graphics"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "f5004f42-377f-4682-92f8-c43178090d7b",
   "metadata": {},
   "outputs": [],
   "source": [
    "thumbnails = get_pubmed_central_open_access_graphics(\n",
    "    citation.pubmed_central_id,\n",
    "    archive_dirname,\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "aaca2c2d-0f4d-44b5-a5da-c8bd7576cdaa",
   "metadata": {},
   "source": [
    "### 3.12. Add the thumbnails to the metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "eddfa837-b785-493e-bccc-4f912e2e01de",
   "metadata": {},
   "outputs": [],
   "source": [
    "metadata['thumbnails'] = [os.path.relpath(thumbnail.filename, archive_dirname) for thumbnail in thumbnails]"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fc41da1a-fa19-4567-bac9-a116d0462efe",
   "metadata": {
    "tags": []
   },
   "source": [
    "### 3.13. Save metadata about the model to an RDF file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "308db37a-e0ed-4f6d-bbc5-a26c0b87fceb",
   "metadata": {},
   "outputs": [],
   "source": [
    "from biosimulators_utils.omex_meta.io import BiosimulationsOmexMetaWriter"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "id": "5b4e4562-6e49-46d3-acae-18bf8fef9961",
   "metadata": {},
   "outputs": [],
   "source": [
    "metadata_filename = os.path.join(archive_dirname, 'metadata.rdf')\n",
    "BiosimulationsOmexMetaWriter().run([metadata], metadata_filename)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "753baabc-467b-48fe-bae8-6058ad7daca2",
   "metadata": {
    "tags": []
   },
   "source": [
    "### 3.14. Create a description of the desired COMBINE/OMEX archive"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "id": "3a0b8404-13c7-46af-a2c9-6beccfa5870e",
   "metadata": {},
   "outputs": [],
   "source": [
    "from biosimulators_utils.combine.data_model import CombineArchive, CombineArchiveContent, CombineArchiveContentFormat"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "id": "01f92e50-3394-4eeb-b81e-bf540b54b279",
   "metadata": {},
   "outputs": [],
   "source": [
    "# initialize the archive\n",
    "archive = CombineArchive()\n",
    "\n",
    "# add the model file to the archive\n",
    "archive.contents.append(CombineArchiveContent(\n",
    "    location=os.path.basename(model_filename),\n",
    "    format=CombineArchiveContentFormat.SBML.value,\n",
    "))\n",
    "\n",
    "# add the SED-ML file to the archive\n",
    "archive.contents.append(CombineArchiveContent(\n",
    "    location='simulation.sedml',\n",
    "    format=CombineArchiveContentFormat.SED_ML.value,\n",
    "    master=True,\n",
    "))\n",
    "\n",
    "# add the RDF metadata file to the archive\n",
    "archive.contents.append(CombineArchiveContent(\n",
    "    location='metadata.rdf',\n",
    "    format=CombineArchiveContentFormat.OMEX_METADATA.value,\n",
    "))\n",
    "\n",
    "# add thumbnails to the archive\n",
    "for thumbnail in thumbnails:\n",
    "    archive.contents.append(CombineArchiveContent(\n",
    "        location=os.path.relpath(thumbnail.filename, archive_dirname),\n",
    "        format=CombineArchiveContentFormat.JPEG.value,\n",
    "    ))"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "41bd0f2d-4a3a-474f-bc89-4e88c59316d5",
   "metadata": {},
   "source": [
    "### 3.15. Export the COMBINE/OMEX archive to a file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "id": "c0e4fab2-f309-496d-97da-84cc16e58660",
   "metadata": {},
   "outputs": [],
   "source": [
    "from biosimulators_utils.combine.io import CombineArchiveWriter"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "id": "67edbb03-154c-433b-b936-94455c637b77",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "_, archive_filename = tempfile.mkstemp(dir='tmp/', suffix='.omex')\n",
    "CombineArchiveWriter().run(archive, archive_dirname, archive_filename)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "dfd92020-b179-4835-a66b-e87aae1a5d0f",
   "metadata": {},
   "source": [
    "### 3.16. Inspect the COMBINE/OMEX archive"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "id": "c20a852c-d35f-4840-a69f-83964b5ae216",
   "metadata": {},
   "outputs": [],
   "source": [
    "from IPython.display import FileLink, FileLinks"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "id": "abee0160-b3e1-489d-b07b-32085123fd7b",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "tmp/tmpdvzzdcf3/<br>\n",
       "&nbsp;&nbsp;<a href='tmp/tmpdvzzdcf3/metadata.rdf' target='_blank'>metadata.rdf</a><br>\n",
       "&nbsp;&nbsp;<a href='tmp/tmpdvzzdcf3/simulation.sedml' target='_blank'>simulation.sedml</a><br>\n",
       "&nbsp;&nbsp;<a href='tmp/tmpdvzzdcf3/PMC3751080.tar.gz' target='_blank'>PMC3751080.tar.gz</a><br>\n",
       "&nbsp;&nbsp;<a href='tmp/tmpdvzzdcf3/Escherichia-coli-core-metabolism.xml' target='_blank'>Escherichia-coli-core-metabolism.xml</a><br>\n",
       "tmp/tmpdvzzdcf3/PMC3751080/<br>\n",
       "&nbsp;&nbsp;<a href='tmp/tmpdvzzdcf3/PMC3751080/1752-0509-7-74-1.gif' target='_blank'>1752-0509-7-74-1.gif</a><br>\n",
       "&nbsp;&nbsp;<a href='tmp/tmpdvzzdcf3/PMC3751080/1752-0509-7-74-2.gif' target='_blank'>1752-0509-7-74-2.gif</a><br>\n",
       "&nbsp;&nbsp;<a href='tmp/tmpdvzzdcf3/PMC3751080/1752-0509-7-74-2.jpg' target='_blank'>1752-0509-7-74-2.jpg</a><br>\n",
       "&nbsp;&nbsp;<a href='tmp/tmpdvzzdcf3/PMC3751080/1752-0509-7-74.pdf' target='_blank'>1752-0509-7-74.pdf</a><br>\n",
       "&nbsp;&nbsp;<a href='tmp/tmpdvzzdcf3/PMC3751080/1752-0509-7-74-1.jpg' target='_blank'>1752-0509-7-74-1.jpg</a><br>\n",
       "&nbsp;&nbsp;<a href='tmp/tmpdvzzdcf3/PMC3751080/1752-0509-7-74.nxml' target='_blank'>1752-0509-7-74.nxml</a><br>"
      ],
      "text/plain": [
       "tmp/tmpdvzzdcf3/\n",
       "  metadata.rdf\n",
       "  simulation.sedml\n",
       "  PMC3751080.tar.gz\n",
       "  Escherichia-coli-core-metabolism.xml\n",
       "tmp/tmpdvzzdcf3/PMC3751080/\n",
       "  1752-0509-7-74-1.gif\n",
       "  1752-0509-7-74-2.gif\n",
       "  1752-0509-7-74-2.jpg\n",
       "  1752-0509-7-74.pdf\n",
       "  1752-0509-7-74-1.jpg\n",
       "  1752-0509-7-74.nxml"
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "FileLinks(archive_dirname)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "id": "5e241523-0cc2-4b5b-bc89-85f4384c7f6f",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<a href='/home/jonrkarr/Documents/Biosimulators_tutorials/tutorials/2. Creating simulations/tmp/tmp20cdr_uv.omex' target='_blank'>/home/jonrkarr/Documents/Biosimulators_tutorials/tutorials/2. Creating simulations/tmp/tmp20cdr_uv.omex</a><br>"
      ],
      "text/plain": [
       "/home/jonrkarr/Documents/Biosimulators_tutorials/tutorials/2. Creating simulations/tmp/tmp20cdr_uv.omex"
      ]
     },
     "execution_count": 33,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "FileLink(archive_filename)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4781e80c-fbc0-43b2-a8a6-f85c6c2c9d95",
   "metadata": {},
   "source": [
    "### 3.16. Verify the COMBINE/OMEX archive "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "270acef6-bb24-4cc7-b3a8-a38c7c6515e8",
   "metadata": {},
   "source": [
    "Execute the archive with [CBMpy](https://biosimulators.org/simulators/cbmpy) and [COBRApy](https://biosimulators.org/simulators/cobrapy)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "id": "c119e4bd-c67e-4f52-8529-5dcb4135d11a",
   "metadata": {
    "scrolled": true,
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "INFO: No xlwt module available, Excel spreadsheet creation disabled\n",
      "\n",
      "\n",
      "\n",
      "No module named 'cplex'\n",
      "\n",
      "\n",
      "\n",
      "CPLEX not available\n",
      "\n",
      "*****\n",
      "Using GLPK\n",
      "*****\n",
      "\n",
      "\n",
      "INFO: No xlrd module available, Excel spreadsheet reading disabled\n",
      "\n",
      "CBMPy environment\n",
      "******************\n",
      "Revision: r689\n",
      "\n",
      "\n",
      "***********************************************************************\n",
      "* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling       *\n",
      "*                http://cbmpy.sourceforge.net                         *\n",
      "* Copyright(C) Brett G. Olivier 2014 - 2019                           *\n",
      "* Dept. of Systems Bioinformatics                                     *\n",
      "* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands            *\n",
      "* CBMPy is developed as part of the BeBasic MetaToolKit Project       *\n",
      "* Distributed under the GNU GPL v 3.0 licence, see                    *\n",
      "* LICENCE (supplied with this release) for details                    *\n",
      "***********************************************************************\n",
      "\n"
     ]
    }
   ],
   "source": [
    "from biosimulators_utils.config import Config\n",
    "import biosimulators_cbmpy\n",
    "import biosimulators_cobrapy"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "id": "d4cfdda0-aa1c-439a-8a96-7fa1b1a09863",
   "metadata": {
    "scrolled": true,
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 2 reports, and 0 plots:\n",
      "  simulation.sedml:\n",
      "    Tasks (1):\n",
      "      task\n",
      "    Reports (2):\n",
      "      objective: 1 data sets\n",
      "      reaction_fluxes: 95 data sets\n",
      "\n",
      "Executing SED-ML file 1: simulation.sedml ...\n",
      "  Found 1 tasks and 2 outputs:\n",
      "    Tasks:\n",
      "      `task`\n",
      "    Outputs:\n",
      "      `objective`\n",
      "      `reaction_fluxes`\n",
      "  Executing task 1: `task`\n",
      "    Executing simulation ..."
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/jonrkarr/Documents/Biosimulators_utils/biosimulators_utils/warnings.py:31: StandardOutputNotLoggedWarning: \u001b[33mStandard output and error could not be logged because capturer is not installed. To install capturer, install BioSimulators utils with the `logging` option (`pip install biosimulators-utils[logging]`).\u001b[0m\n",
      "  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n",
      "/home/jonrkarr/Documents/Biosimulators_utils/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mCOMBINE/OMEX archive may be invalid.\n",
      "  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.\u001b[0m\n",
      "  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n",
      "/home/jonrkarr/Documents/Biosimulators_utils/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\n",
      "  - Model `model` may be invalid.\n",
      "    - The model file `Escherichia-coli-core-metabolism.xml` may be invalid.\n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <compartment> 'c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\n",
      "        Reference: L3V1 Section 4.5\n",
      "         The <compartment> 'c' has no discernable units.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <compartment> 'e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\n",
      "        Reference: L3V1 Section 4.5\n",
      "         The <compartment> 'e' has no discernable units.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_13dpg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_13dpg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_2pg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_2pg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_3pg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_3pg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_6pgc_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_6pgc_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_6pgl_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_6pgl_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_ac_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_ac_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_ac_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_ac_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_acald_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_acald_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_acald_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_acald_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_accoa_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_accoa_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_acon_C_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_acon_C_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_actp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_actp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_adp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_adp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_akg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_akg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_akg_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_akg_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_amp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_amp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_atp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_atp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_cit_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_cit_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_co2_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_co2_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_co2_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_co2_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_coa_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_coa_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_dhap_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_dhap_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_e4p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_e4p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_etoh_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_etoh_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_etoh_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_etoh_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_f6p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_f6p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_fdp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_fdp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_for_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_for_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_for_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_for_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_fru_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_fru_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_fum_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_fum_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_fum_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_fum_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_g3p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_g3p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_g6p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_g6p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_glc__D_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_glc__D_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_gln__L_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_gln__L_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_gln__L_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_gln__L_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_glu__L_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_glu__L_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_glu__L_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_glu__L_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_glx_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_glx_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_h2o_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_h2o_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_h2o_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_h2o_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_h_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_h_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_h_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_h_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_icit_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_icit_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_lac__D_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_lac__D_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_lac__D_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_lac__D_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_mal__L_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_mal__L_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_mal__L_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_mal__L_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_nad_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_nad_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_nadh_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_nadh_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_nadp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_nadp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_nadph_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_nadph_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_nh4_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_nh4_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_nh4_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_nh4_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_o2_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_o2_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_o2_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_o2_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_oaa_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_oaa_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_pep_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_pep_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_pi_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_pi_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_pi_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_pi_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_pyr_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_pyr_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_pyr_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_pyr_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_q8_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_q8_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_q8h2_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_q8h2_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_r5p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_r5p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_ru5p__D_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_ru5p__D_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_s7p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_s7p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_succ_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_succ_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_succ_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_succ_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_succoa_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_succoa_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "         The units of the <species> 'M_xu5p__D_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "        \n",
      "      - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "        Reference: L3V1 Section 4.6.5\n",
      "         The <species> with id 'M_xu5p__D_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_13dpg_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_2pg_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_3pg_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_6pgc_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_6pgl_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_ac_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_ac_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_acald_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_acald_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_accoa_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_acon_C_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_actp_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_adp_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_akg_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_akg_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_amp_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_atp_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_cit_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_co2_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_co2_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_coa_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_dhap_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_e4p_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_etoh_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_etoh_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_f6p_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_fdp_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_for_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_for_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_fru_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_fum_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_fum_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_g3p_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_g6p_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_glc__D_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_gln__L_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_gln__L_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_glu__L_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_glu__L_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_glx_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_h2o_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_h2o_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_h_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_h_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_icit_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_lac__D_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_lac__D_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_mal__L_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_mal__L_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_nad_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_nadh_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_nadp_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_nadph_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_nh4_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_nh4_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_o2_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_o2_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_oaa_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_pep_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_pi_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_pi_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_pyr_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_pyr_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_q8_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_q8h2_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_r5p_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_ru5p__D_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_s7p_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_succ_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_succ_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_succoa_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "      - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "         The <species> with the id 'M_xu5p__D_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "        \n",
      "    - The changes of the model may be invalid.\n",
      "      - Change 1 may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change 2 may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change 3 may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change 4 may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change 5 may be invalid.\n",
      "        - XPath could not be validated.\n",
      "  - Data generator `data_generator_obj` may be invalid.\n",
      "    - Variable `variable_obj` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ACALD` may be invalid.\n",
      "    - Variable `variable_R_ACALD` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ACALDt` may be invalid.\n",
      "    - Variable `variable_R_ACALDt` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ACKr` may be invalid.\n",
      "    - Variable `variable_R_ACKr` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ACONTa` may be invalid.\n",
      "    - Variable `variable_R_ACONTa` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ACONTb` may be invalid.\n",
      "    - Variable `variable_R_ACONTb` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ACt2r` may be invalid.\n",
      "    - Variable `variable_R_ACt2r` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ADK1` may be invalid.\n",
      "    - Variable `variable_R_ADK1` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_AKGDH` may be invalid.\n",
      "    - Variable `variable_R_AKGDH` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_AKGt2r` may be invalid.\n",
      "    - Variable `variable_R_AKGt2r` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ALCD2x` may be invalid.\n",
      "    - Variable `variable_R_ALCD2x` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ATPM` may be invalid.\n",
      "    - Variable `variable_R_ATPM` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ATPS4r` may be invalid.\n",
      "    - Variable `variable_R_ATPS4r` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_Biomass_Ecoli_core` may be invalid.\n",
      "    - Variable `variable_R_Biomass_Ecoli_core` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_CO2t` may be invalid.\n",
      "    - Variable `variable_R_CO2t` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_CS` may be invalid.\n",
      "    - Variable `variable_R_CS` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_CYTBD` may be invalid.\n",
      "    - Variable `variable_R_CYTBD` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_D_LACt2` may be invalid.\n",
      "    - Variable `variable_R_D_LACt2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ENO` may be invalid.\n",
      "    - Variable `variable_R_ENO` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ETOHt2r` may be invalid.\n",
      "    - Variable `variable_R_ETOHt2r` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_ac_e` may be invalid.\n",
      "    - Variable `variable_R_EX_ac_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_acald_e` may be invalid.\n",
      "    - Variable `variable_R_EX_acald_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_akg_e` may be invalid.\n",
      "    - Variable `variable_R_EX_akg_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_co2_e` may be invalid.\n",
      "    - Variable `variable_R_EX_co2_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_etoh_e` may be invalid.\n",
      "    - Variable `variable_R_EX_etoh_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_for_e` may be invalid.\n",
      "    - Variable `variable_R_EX_for_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_fru_e` may be invalid.\n",
      "    - Variable `variable_R_EX_fru_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_fum_e` may be invalid.\n",
      "    - Variable `variable_R_EX_fum_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_glc__D_e` may be invalid.\n",
      "    - Variable `variable_R_EX_glc__D_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_gln__L_e` may be invalid.\n",
      "    - Variable `variable_R_EX_gln__L_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_glu__L_e` may be invalid.\n",
      "    - Variable `variable_R_EX_glu__L_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_h_e` may be invalid.\n",
      "    - Variable `variable_R_EX_h_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_h2o_e` may be invalid.\n",
      "    - Variable `variable_R_EX_h2o_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_lac__D_e` may be invalid.\n",
      "    - Variable `variable_R_EX_lac__D_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_mal__L_e` may be invalid.\n",
      "    - Variable `variable_R_EX_mal__L_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_nh4_e` may be invalid.\n",
      "    - Variable `variable_R_EX_nh4_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_o2_e` may be invalid.\n",
      "    - Variable `variable_R_EX_o2_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_pi_e` may be invalid.\n",
      "    - Variable `variable_R_EX_pi_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_pyr_e` may be invalid.\n",
      "    - Variable `variable_R_EX_pyr_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_succ_e` may be invalid.\n",
      "    - Variable `variable_R_EX_succ_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FBA` may be invalid.\n",
      "    - Variable `variable_R_FBA` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FBP` may be invalid.\n",
      "    - Variable `variable_R_FBP` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FORt2` may be invalid.\n",
      "    - Variable `variable_R_FORt2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FORti` may be invalid.\n",
      "    - Variable `variable_R_FORti` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FRD7` may be invalid.\n",
      "    - Variable `variable_R_FRD7` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FRUpts2` may be invalid.\n",
      "    - Variable `variable_R_FRUpts2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FUM` may be invalid.\n",
      "    - Variable `variable_R_FUM` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FUMt2_2` may be invalid.\n",
      "    - Variable `variable_R_FUMt2_2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_G6PDH2r` may be invalid.\n",
      "    - Variable `variable_R_G6PDH2r` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GAPD` may be invalid.\n",
      "    - Variable `variable_R_GAPD` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GLCpts` may be invalid.\n",
      "    - Variable `variable_R_GLCpts` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GLNS` may be invalid.\n",
      "    - Variable `variable_R_GLNS` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GLNabc` may be invalid.\n",
      "    - Variable `variable_R_GLNabc` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GLUDy` may be invalid.\n",
      "    - Variable `variable_R_GLUDy` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GLUN` may be invalid.\n",
      "    - Variable `variable_R_GLUN` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GLUSy` may be invalid.\n",
      "    - Variable `variable_R_GLUSy` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GLUt2r` may be invalid.\n",
      "    - Variable `variable_R_GLUt2r` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GND` may be invalid.\n",
      "    - Variable `variable_R_GND` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_H2Ot` may be invalid.\n",
      "    - Variable `variable_R_H2Ot` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ICDHyr` may be invalid.\n",
      "    - Variable `variable_R_ICDHyr` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ICL` may be invalid.\n",
      "    - Variable `variable_R_ICL` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_LDH_D` may be invalid.\n",
      "    - Variable `variable_R_LDH_D` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_MALS` may be invalid.\n",
      "    - Variable `variable_R_MALS` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_MALt2_2` may be invalid.\n",
      "    - Variable `variable_R_MALt2_2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_MDH` may be invalid.\n",
      "    - Variable `variable_R_MDH` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ME1` may be invalid.\n",
      "    - Variable `variable_R_ME1` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ME2` may be invalid.\n",
      "    - Variable `variable_R_ME2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_NADH16` may be invalid.\n",
      "    - Variable `variable_R_NADH16` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_NADTRHD` may be invalid.\n",
      "    - Variable `variable_R_NADTRHD` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_NH4t` may be invalid.\n",
      "    - Variable `variable_R_NH4t` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_O2t` may be invalid.\n",
      "    - Variable `variable_R_O2t` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PDH` may be invalid.\n",
      "    - Variable `variable_R_PDH` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PFK` may be invalid.\n",
      "    - Variable `variable_R_PFK` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PFL` may be invalid.\n",
      "    - Variable `variable_R_PFL` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PGI` may be invalid.\n",
      "    - Variable `variable_R_PGI` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PGK` may be invalid.\n",
      "    - Variable `variable_R_PGK` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PGL` may be invalid.\n",
      "    - Variable `variable_R_PGL` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PGM` may be invalid.\n",
      "    - Variable `variable_R_PGM` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PIt2r` may be invalid.\n",
      "    - Variable `variable_R_PIt2r` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PPC` may be invalid.\n",
      "    - Variable `variable_R_PPC` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PPCK` may be invalid.\n",
      "    - Variable `variable_R_PPCK` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PPS` may be invalid.\n",
      "    - Variable `variable_R_PPS` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PTAr` may be invalid.\n",
      "    - Variable `variable_R_PTAr` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PYK` may be invalid.\n",
      "    - Variable `variable_R_PYK` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PYRt2` may be invalid.\n",
      "    - Variable `variable_R_PYRt2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_RPE` may be invalid.\n",
      "    - Variable `variable_R_RPE` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_RPI` may be invalid.\n",
      "    - Variable `variable_R_RPI` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_SUCCt2_2` may be invalid.\n",
      "    - Variable `variable_R_SUCCt2_2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_SUCCt3` may be invalid.\n",
      "    - Variable `variable_R_SUCCt3` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_SUCDi` may be invalid.\n",
      "    - Variable `variable_R_SUCDi` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_SUCOAS` may be invalid.\n",
      "    - Variable `variable_R_SUCOAS` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_TALA` may be invalid.\n",
      "    - Variable `variable_R_TALA` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_THD2` may be invalid.\n",
      "    - Variable `variable_R_THD2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_TKT1` may be invalid.\n",
      "    - Variable `variable_R_TKT1` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_TKT2` may be invalid.\n",
      "    - Variable `variable_R_TKT2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_TPI` may be invalid.\n",
      "    - Variable `variable_R_TPI` may be invalid.\n",
      "      - XPath could not be validated.\u001b[0m\n",
      "  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n",
      "/home/jonrkarr/Documents/Biosimulators_utils/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\n",
      "  - The SED-ML file at location `simulation.sedml` may be invalid.\n",
      "    - Model `model` may be invalid.\n",
      "      - The model file `Escherichia-coli-core-metabolism.xml` may be invalid.\n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <compartment> 'c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\n",
      "          Reference: L3V1 Section 4.5\n",
      "           The <compartment> 'c' has no discernable units.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <compartment> 'e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\n",
      "          Reference: L3V1 Section 4.5\n",
      "           The <compartment> 'e' has no discernable units.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_13dpg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_13dpg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_2pg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_2pg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_3pg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_3pg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_6pgc_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_6pgc_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_6pgl_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_6pgl_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_ac_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_ac_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_ac_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_ac_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_acald_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_acald_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_acald_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_acald_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_accoa_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_accoa_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_acon_C_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_acon_C_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_actp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_actp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_adp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_adp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_akg_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_akg_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_akg_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_akg_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_amp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_amp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_atp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_atp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_cit_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_cit_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_co2_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_co2_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_co2_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_co2_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_coa_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_coa_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_dhap_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_dhap_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_e4p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_e4p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_etoh_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_etoh_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_etoh_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_etoh_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_f6p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_f6p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_fdp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_fdp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_for_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_for_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_for_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_for_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_fru_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_fru_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_fum_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_fum_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_fum_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_fum_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_g3p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_g3p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_g6p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_g6p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_glc__D_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_glc__D_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_gln__L_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_gln__L_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_gln__L_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_gln__L_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_glu__L_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_glu__L_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_glu__L_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_glu__L_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_glx_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_glx_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_h2o_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_h2o_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_h2o_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_h2o_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_h_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_h_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_h_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_h_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_icit_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_icit_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_lac__D_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_lac__D_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_lac__D_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_lac__D_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_mal__L_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_mal__L_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_mal__L_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_mal__L_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_nad_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_nad_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_nadh_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_nadh_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_nadp_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_nadp_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_nadph_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_nadph_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_nh4_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_nh4_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_nh4_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_nh4_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_o2_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_o2_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_o2_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_o2_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_oaa_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_oaa_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_pep_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_pep_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_pi_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_pi_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_pi_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_pi_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_pyr_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_pyr_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_pyr_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_pyr_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_q8_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_q8_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_q8h2_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_q8h2_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_r5p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_r5p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_ru5p__D_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_ru5p__D_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_s7p_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_s7p_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_succ_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_succ_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_succ_e' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_succ_e' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_succoa_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_succoa_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \n",
      "           The units of the <species> 'M_xu5p__D_c' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\n",
      "          \n",
      "        - If the attribute 'substanceUnits' in a Species object has not been set, then the unit of measurement associated with the species' quantity is determined by the value of the enclosing Model object's 'substanceUnits' attribute. If neither the Species object's 'substanceUnits' attribute nor the enclosing Model object's 'substanceUnits' attribute are set, then the unit of that species' quantity is undefined.\n",
      "          Reference: L3V1 Section 4.6.5\n",
      "           The <species> with id 'M_xu5p__D_c' does not have a substanceUnits attribute, nor does its enclosing <model>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_13dpg_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_2pg_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_3pg_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_6pgc_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_6pgl_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_ac_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_ac_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_acald_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_acald_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_accoa_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_acon_C_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_actp_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_adp_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_akg_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_akg_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_amp_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_atp_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_cit_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_co2_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_co2_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_coa_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_dhap_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_e4p_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_etoh_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_etoh_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_f6p_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_fdp_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_for_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_for_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_fru_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_fum_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_fum_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_g3p_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_g6p_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_glc__D_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_gln__L_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_gln__L_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_glu__L_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_glu__L_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_glx_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_h2o_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_h2o_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_h_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_h_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_icit_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_lac__D_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_lac__D_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_mal__L_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_mal__L_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_nad_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_nadh_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_nadp_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_nadph_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_nh4_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_nh4_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_o2_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_o2_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_oaa_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_pep_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_pi_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_pi_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_pyr_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_pyr_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_q8_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_q8h2_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_r5p_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_ru5p__D_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_s7p_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_succ_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_succ_e' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_succoa_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "        - As a principle of best modeling practice, the <species> should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models.\n",
      "           The <species> with the id 'M_xu5p__D_c' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an <initialAssignment> or <assignmentRule>.\n",
      "          \n",
      "      - The changes of the model may be invalid.\n",
      "        - Change 1 may be invalid.\n",
      "          - XPath could not be validated.\n",
      "        - Change 2 may be invalid.\n",
      "          - XPath could not be validated.\n",
      "        - Change 3 may be invalid.\n",
      "          - XPath could not be validated.\n",
      "        - Change 4 may be invalid.\n",
      "          - XPath could not be validated.\n",
      "        - Change 5 may be invalid.\n",
      "          - XPath could not be validated.\n",
      "    - Data generator `data_generator_obj` may be invalid.\n",
      "      - Variable `variable_obj` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_ACALD` may be invalid.\n",
      "      - Variable `variable_R_ACALD` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_ACALDt` may be invalid.\n",
      "      - Variable `variable_R_ACALDt` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_ACKr` may be invalid.\n",
      "      - Variable `variable_R_ACKr` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_ACONTa` may be invalid.\n",
      "      - Variable `variable_R_ACONTa` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_ACONTb` may be invalid.\n",
      "      - Variable `variable_R_ACONTb` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_ACt2r` may be invalid.\n",
      "      - Variable `variable_R_ACt2r` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_ADK1` may be invalid.\n",
      "      - Variable `variable_R_ADK1` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_AKGDH` may be invalid.\n",
      "      - Variable `variable_R_AKGDH` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_AKGt2r` may be invalid.\n",
      "      - Variable `variable_R_AKGt2r` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_ALCD2x` may be invalid.\n",
      "      - Variable `variable_R_ALCD2x` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_ATPM` may be invalid.\n",
      "      - Variable `variable_R_ATPM` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_ATPS4r` may be invalid.\n",
      "      - Variable `variable_R_ATPS4r` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_Biomass_Ecoli_core` may be invalid.\n",
      "      - Variable `variable_R_Biomass_Ecoli_core` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_CO2t` may be invalid.\n",
      "      - Variable `variable_R_CO2t` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_CS` may be invalid.\n",
      "      - Variable `variable_R_CS` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_CYTBD` may be invalid.\n",
      "      - Variable `variable_R_CYTBD` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_D_LACt2` may be invalid.\n",
      "      - Variable `variable_R_D_LACt2` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_ENO` may be invalid.\n",
      "      - Variable `variable_R_ENO` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_ETOHt2r` may be invalid.\n",
      "      - Variable `variable_R_ETOHt2r` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_EX_ac_e` may be invalid.\n",
      "      - Variable `variable_R_EX_ac_e` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_EX_acald_e` may be invalid.\n",
      "      - Variable `variable_R_EX_acald_e` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_EX_akg_e` may be invalid.\n",
      "      - Variable `variable_R_EX_akg_e` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_EX_co2_e` may be invalid.\n",
      "      - Variable `variable_R_EX_co2_e` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_EX_etoh_e` may be invalid.\n",
      "      - Variable `variable_R_EX_etoh_e` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_EX_for_e` may be invalid.\n",
      "      - Variable `variable_R_EX_for_e` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_EX_fru_e` may be invalid.\n",
      "      - Variable `variable_R_EX_fru_e` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_EX_fum_e` may be invalid.\n",
      "      - Variable `variable_R_EX_fum_e` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_EX_glc__D_e` may be invalid.\n",
      "      - Variable `variable_R_EX_glc__D_e` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_EX_gln__L_e` may be invalid.\n",
      "      - Variable `variable_R_EX_gln__L_e` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_EX_glu__L_e` may be invalid.\n",
      "      - Variable `variable_R_EX_glu__L_e` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_EX_h_e` may be invalid.\n",
      "      - Variable `variable_R_EX_h_e` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_EX_h2o_e` may be invalid.\n",
      "      - Variable `variable_R_EX_h2o_e` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_EX_lac__D_e` may be invalid.\n",
      "      - Variable `variable_R_EX_lac__D_e` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_EX_mal__L_e` may be invalid.\n",
      "      - Variable `variable_R_EX_mal__L_e` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_EX_nh4_e` may be invalid.\n",
      "      - Variable `variable_R_EX_nh4_e` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_EX_o2_e` may be invalid.\n",
      "      - Variable `variable_R_EX_o2_e` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_EX_pi_e` may be invalid.\n",
      "      - Variable `variable_R_EX_pi_e` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_EX_pyr_e` may be invalid.\n",
      "      - Variable `variable_R_EX_pyr_e` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_EX_succ_e` may be invalid.\n",
      "      - Variable `variable_R_EX_succ_e` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_FBA` may be invalid.\n",
      "      - Variable `variable_R_FBA` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_FBP` may be invalid.\n",
      "      - Variable `variable_R_FBP` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_FORt2` may be invalid.\n",
      "      - Variable `variable_R_FORt2` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_FORti` may be invalid.\n",
      "      - Variable `variable_R_FORti` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_FRD7` may be invalid.\n",
      "      - Variable `variable_R_FRD7` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_FRUpts2` may be invalid.\n",
      "      - Variable `variable_R_FRUpts2` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_FUM` may be invalid.\n",
      "      - Variable `variable_R_FUM` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_FUMt2_2` may be invalid.\n",
      "      - Variable `variable_R_FUMt2_2` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_G6PDH2r` may be invalid.\n",
      "      - Variable `variable_R_G6PDH2r` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_GAPD` may be invalid.\n",
      "      - Variable `variable_R_GAPD` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_GLCpts` may be invalid.\n",
      "      - Variable `variable_R_GLCpts` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_GLNS` may be invalid.\n",
      "      - Variable `variable_R_GLNS` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_GLNabc` may be invalid.\n",
      "      - Variable `variable_R_GLNabc` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_GLUDy` may be invalid.\n",
      "      - Variable `variable_R_GLUDy` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_GLUN` may be invalid.\n",
      "      - Variable `variable_R_GLUN` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_GLUSy` may be invalid.\n",
      "      - Variable `variable_R_GLUSy` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_GLUt2r` may be invalid.\n",
      "      - Variable `variable_R_GLUt2r` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_GND` may be invalid.\n",
      "      - Variable `variable_R_GND` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_H2Ot` may be invalid.\n",
      "      - Variable `variable_R_H2Ot` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_ICDHyr` may be invalid.\n",
      "      - Variable `variable_R_ICDHyr` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_ICL` may be invalid.\n",
      "      - Variable `variable_R_ICL` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_LDH_D` may be invalid.\n",
      "      - Variable `variable_R_LDH_D` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_MALS` may be invalid.\n",
      "      - Variable `variable_R_MALS` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_MALt2_2` may be invalid.\n",
      "      - Variable `variable_R_MALt2_2` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_MDH` may be invalid.\n",
      "      - Variable `variable_R_MDH` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_ME1` may be invalid.\n",
      "      - Variable `variable_R_ME1` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_ME2` may be invalid.\n",
      "      - Variable `variable_R_ME2` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_NADH16` may be invalid.\n",
      "      - Variable `variable_R_NADH16` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_NADTRHD` may be invalid.\n",
      "      - Variable `variable_R_NADTRHD` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_NH4t` may be invalid.\n",
      "      - Variable `variable_R_NH4t` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_O2t` may be invalid.\n",
      "      - Variable `variable_R_O2t` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_PDH` may be invalid.\n",
      "      - Variable `variable_R_PDH` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_PFK` may be invalid.\n",
      "      - Variable `variable_R_PFK` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_PFL` may be invalid.\n",
      "      - Variable `variable_R_PFL` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_PGI` may be invalid.\n",
      "      - Variable `variable_R_PGI` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_PGK` may be invalid.\n",
      "      - Variable `variable_R_PGK` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_PGL` may be invalid.\n",
      "      - Variable `variable_R_PGL` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_PGM` may be invalid.\n",
      "      - Variable `variable_R_PGM` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_PIt2r` may be invalid.\n",
      "      - Variable `variable_R_PIt2r` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_PPC` may be invalid.\n",
      "      - Variable `variable_R_PPC` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_PPCK` may be invalid.\n",
      "      - Variable `variable_R_PPCK` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_PPS` may be invalid.\n",
      "      - Variable `variable_R_PPS` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_PTAr` may be invalid.\n",
      "      - Variable `variable_R_PTAr` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_PYK` may be invalid.\n",
      "      - Variable `variable_R_PYK` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_PYRt2` may be invalid.\n",
      "      - Variable `variable_R_PYRt2` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_RPE` may be invalid.\n",
      "      - Variable `variable_R_RPE` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_RPI` may be invalid.\n",
      "      - Variable `variable_R_RPI` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_SUCCt2_2` may be invalid.\n",
      "      - Variable `variable_R_SUCCt2_2` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_SUCCt3` may be invalid.\n",
      "      - Variable `variable_R_SUCCt3` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_SUCDi` may be invalid.\n",
      "      - Variable `variable_R_SUCDi` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_SUCOAS` may be invalid.\n",
      "      - Variable `variable_R_SUCOAS` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_TALA` may be invalid.\n",
      "      - Variable `variable_R_TALA` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_THD2` may be invalid.\n",
      "      - Variable `variable_R_THD2` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_TKT1` may be invalid.\n",
      "      - Variable `variable_R_TKT1` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_TKT2` may be invalid.\n",
      "      - Variable `variable_R_TKT2` may be invalid.\n",
      "        - XPath could not be validated.\n",
      "    - Data generator `data_generator_R_TPI` may be invalid.\n",
      "      - Variable `variable_R_TPI` may be invalid.\n",
      "        - XPath could not be validated.\u001b[0m\n",
      "  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n",
      "/home/jonrkarr/Documents/Biosimulators_utils/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\n",
      "  - Model `model` may be invalid.\n",
      "    - The changes of the model may be invalid.\n",
      "      - Change 1 may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change 2 may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change 3 may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change 4 may be invalid.\n",
      "        - XPath could not be validated.\n",
      "      - Change 5 may be invalid.\n",
      "        - XPath could not be validated.\n",
      "  - Data generator `data_generator_obj` may be invalid.\n",
      "    - Variable `variable_obj` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ACALD` may be invalid.\n",
      "    - Variable `variable_R_ACALD` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ACALDt` may be invalid.\n",
      "    - Variable `variable_R_ACALDt` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ACKr` may be invalid.\n",
      "    - Variable `variable_R_ACKr` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ACONTa` may be invalid.\n",
      "    - Variable `variable_R_ACONTa` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ACONTb` may be invalid.\n",
      "    - Variable `variable_R_ACONTb` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ACt2r` may be invalid.\n",
      "    - Variable `variable_R_ACt2r` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ADK1` may be invalid.\n",
      "    - Variable `variable_R_ADK1` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_AKGDH` may be invalid.\n",
      "    - Variable `variable_R_AKGDH` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_AKGt2r` may be invalid.\n",
      "    - Variable `variable_R_AKGt2r` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ALCD2x` may be invalid.\n",
      "    - Variable `variable_R_ALCD2x` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ATPM` may be invalid.\n",
      "    - Variable `variable_R_ATPM` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ATPS4r` may be invalid.\n",
      "    - Variable `variable_R_ATPS4r` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_Biomass_Ecoli_core` may be invalid.\n",
      "    - Variable `variable_R_Biomass_Ecoli_core` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_CO2t` may be invalid.\n",
      "    - Variable `variable_R_CO2t` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_CS` may be invalid.\n",
      "    - Variable `variable_R_CS` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_CYTBD` may be invalid.\n",
      "    - Variable `variable_R_CYTBD` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_D_LACt2` may be invalid.\n",
      "    - Variable `variable_R_D_LACt2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ENO` may be invalid.\n",
      "    - Variable `variable_R_ENO` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ETOHt2r` may be invalid.\n",
      "    - Variable `variable_R_ETOHt2r` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_ac_e` may be invalid.\n",
      "    - Variable `variable_R_EX_ac_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_acald_e` may be invalid.\n",
      "    - Variable `variable_R_EX_acald_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_akg_e` may be invalid.\n",
      "    - Variable `variable_R_EX_akg_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_co2_e` may be invalid.\n",
      "    - Variable `variable_R_EX_co2_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_etoh_e` may be invalid.\n",
      "    - Variable `variable_R_EX_etoh_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_for_e` may be invalid.\n",
      "    - Variable `variable_R_EX_for_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_fru_e` may be invalid.\n",
      "    - Variable `variable_R_EX_fru_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_fum_e` may be invalid.\n",
      "    - Variable `variable_R_EX_fum_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_glc__D_e` may be invalid.\n",
      "    - Variable `variable_R_EX_glc__D_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_gln__L_e` may be invalid.\n",
      "    - Variable `variable_R_EX_gln__L_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_glu__L_e` may be invalid.\n",
      "    - Variable `variable_R_EX_glu__L_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_h_e` may be invalid.\n",
      "    - Variable `variable_R_EX_h_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_h2o_e` may be invalid.\n",
      "    - Variable `variable_R_EX_h2o_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_lac__D_e` may be invalid.\n",
      "    - Variable `variable_R_EX_lac__D_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_mal__L_e` may be invalid.\n",
      "    - Variable `variable_R_EX_mal__L_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_nh4_e` may be invalid.\n",
      "    - Variable `variable_R_EX_nh4_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_o2_e` may be invalid.\n",
      "    - Variable `variable_R_EX_o2_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_pi_e` may be invalid.\n",
      "    - Variable `variable_R_EX_pi_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_pyr_e` may be invalid.\n",
      "    - Variable `variable_R_EX_pyr_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_EX_succ_e` may be invalid.\n",
      "    - Variable `variable_R_EX_succ_e` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FBA` may be invalid.\n",
      "    - Variable `variable_R_FBA` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FBP` may be invalid.\n",
      "    - Variable `variable_R_FBP` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FORt2` may be invalid.\n",
      "    - Variable `variable_R_FORt2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FORti` may be invalid.\n",
      "    - Variable `variable_R_FORti` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FRD7` may be invalid.\n",
      "    - Variable `variable_R_FRD7` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FRUpts2` may be invalid.\n",
      "    - Variable `variable_R_FRUpts2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FUM` may be invalid.\n",
      "    - Variable `variable_R_FUM` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_FUMt2_2` may be invalid.\n",
      "    - Variable `variable_R_FUMt2_2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_G6PDH2r` may be invalid.\n",
      "    - Variable `variable_R_G6PDH2r` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GAPD` may be invalid.\n",
      "    - Variable `variable_R_GAPD` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GLCpts` may be invalid.\n",
      "    - Variable `variable_R_GLCpts` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GLNS` may be invalid.\n",
      "    - Variable `variable_R_GLNS` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GLNabc` may be invalid.\n",
      "    - Variable `variable_R_GLNabc` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GLUDy` may be invalid.\n",
      "    - Variable `variable_R_GLUDy` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GLUN` may be invalid.\n",
      "    - Variable `variable_R_GLUN` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GLUSy` may be invalid.\n",
      "    - Variable `variable_R_GLUSy` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GLUt2r` may be invalid.\n",
      "    - Variable `variable_R_GLUt2r` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_GND` may be invalid.\n",
      "    - Variable `variable_R_GND` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_H2Ot` may be invalid.\n",
      "    - Variable `variable_R_H2Ot` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ICDHyr` may be invalid.\n",
      "    - Variable `variable_R_ICDHyr` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ICL` may be invalid.\n",
      "    - Variable `variable_R_ICL` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_LDH_D` may be invalid.\n",
      "    - Variable `variable_R_LDH_D` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_MALS` may be invalid.\n",
      "    - Variable `variable_R_MALS` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_MALt2_2` may be invalid.\n",
      "    - Variable `variable_R_MALt2_2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_MDH` may be invalid.\n",
      "    - Variable `variable_R_MDH` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ME1` may be invalid.\n",
      "    - Variable `variable_R_ME1` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_ME2` may be invalid.\n",
      "    - Variable `variable_R_ME2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_NADH16` may be invalid.\n",
      "    - Variable `variable_R_NADH16` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_NADTRHD` may be invalid.\n",
      "    - Variable `variable_R_NADTRHD` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_NH4t` may be invalid.\n",
      "    - Variable `variable_R_NH4t` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_O2t` may be invalid.\n",
      "    - Variable `variable_R_O2t` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PDH` may be invalid.\n",
      "    - Variable `variable_R_PDH` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PFK` may be invalid.\n",
      "    - Variable `variable_R_PFK` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PFL` may be invalid.\n",
      "    - Variable `variable_R_PFL` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PGI` may be invalid.\n",
      "    - Variable `variable_R_PGI` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PGK` may be invalid.\n",
      "    - Variable `variable_R_PGK` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PGL` may be invalid.\n",
      "    - Variable `variable_R_PGL` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PGM` may be invalid.\n",
      "    - Variable `variable_R_PGM` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PIt2r` may be invalid.\n",
      "    - Variable `variable_R_PIt2r` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PPC` may be invalid.\n",
      "    - Variable `variable_R_PPC` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PPCK` may be invalid.\n",
      "    - Variable `variable_R_PPCK` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PPS` may be invalid.\n",
      "    - Variable `variable_R_PPS` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PTAr` may be invalid.\n",
      "    - Variable `variable_R_PTAr` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PYK` may be invalid.\n",
      "    - Variable `variable_R_PYK` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_PYRt2` may be invalid.\n",
      "    - Variable `variable_R_PYRt2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_RPE` may be invalid.\n",
      "    - Variable `variable_R_RPE` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_RPI` may be invalid.\n",
      "    - Variable `variable_R_RPI` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_SUCCt2_2` may be invalid.\n",
      "    - Variable `variable_R_SUCCt2_2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_SUCCt3` may be invalid.\n",
      "    - Variable `variable_R_SUCCt3` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_SUCDi` may be invalid.\n",
      "    - Variable `variable_R_SUCDi` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_SUCOAS` may be invalid.\n",
      "    - Variable `variable_R_SUCOAS` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_TALA` may be invalid.\n",
      "    - Variable `variable_R_TALA` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_THD2` may be invalid.\n",
      "    - Variable `variable_R_THD2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_TKT1` may be invalid.\n",
      "    - Variable `variable_R_TKT1` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_TKT2` may be invalid.\n",
      "    - Variable `variable_R_TKT2` may be invalid.\n",
      "      - XPath could not be validated.\n",
      "  - Data generator `data_generator_R_TPI` may be invalid.\n",
      "    - Variable `variable_R_TPI` may be invalid.\n",
      "      - XPath could not be validated.\u001b[0m\n",
      "  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "FBC version: 2\n",
      "M.getNumReactions: 95\n",
      "M.getNumSpecies: 72\n",
      "FBC.getNumObjectives: 1\n",
      "FBC.getNumParameters: 5\n",
      "FBC.getNumGeneProducts: 137\n",
      "Zero dimension compartment detected: c\n",
      "Zero dimension compartment detected: e\n",
      "FluxBounds process1: 0.003\n",
      "INFO: Active objective: obj\n",
      "Adding objective: obj\n",
      "FluxBounds process2: 0.001\n",
      "\n",
      "SBML3 load time: 0.073\n",
      "\n",
      "\n",
      "gplk_constructLPfromFBA time: 0.0029625892639160156\n",
      "\n",
      "\n",
      "glpk_analyzeModel FBA --> LP time: 2.384185791015625e-07\n",
      "\n",
      "\n",
      "analyzeModel objective value: 0.8739215069684909\n",
      "\n",
      "Objective obj: \"maximize\"\n",
      " \u001b[34msucceeded\u001b[0m\n",
      "    Generating 2 outputs ...\n",
      "      Generating output 1: `objective` ... \u001b[34msucceeded\u001b[0m\n",
      "      Generating output 2: `reaction_fluxes` ... \u001b[34msucceeded\u001b[0m\n",
      "\n",
      "Bundling outputs ...\n",
      "Cleaning up ...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/jonrkarr/Documents/Biosimulators_utils/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `variable_R_FUMt2_2` may be invalid.\n",
      "  - XPath could not be validated.\n",
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      "  - XPath could not be validated.\u001b[0m\n",
      "  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 2 reports, and 0 plots:\n",
      "  simulation.sedml:\n",
      "    Tasks (1):\n",
      "      task\n",
      "    Reports (2):\n",
      "      objective: 1 data sets\n",
      "      reaction_fluxes: 95 data sets\n",
      "\n",
      "Executing SED-ML file 1: simulation.sedml ...\n",
      "  Found 1 tasks and 2 outputs:\n",
      "    Tasks:\n",
      "      `task`\n",
      "    Outputs:\n",
      "      `objective`\n",
      "      `reaction_fluxes`\n",
      "  Executing task 1: `task`\n",
      "    Executing simulation ...Academic license - for non-commercial use only - expires 2022-09-04\n",
      "Using license file /home/jonrkarr/gurobi.lic\n",
      " \u001b[34msucceeded\u001b[0m\n",
      "    Generating 2 outputs ...\n",
      "      Generating output 1: `objective` ... \u001b[34msucceeded\u001b[0m\n",
      "      Generating output 2: `reaction_fluxes` ... \u001b[34msucceeded\u001b[0m\n",
      "\n",
      "Bundling outputs ...\n",
      "Cleaning up ...\n"
     ]
    }
   ],
   "source": [
    "output_dirname = tempfile.mkdtemp(dir='tmp/')\n",
    "config = Config(\n",
    "    COLLECT_COMBINE_ARCHIVE_RESULTS=True,\n",
    "    LOG=False,\n",
    ")\n",
    "\n",
    "results_cbmpy, _ = biosimulators_cbmpy.exec_sedml_docs_in_combine_archive(archive_filename, output_dirname, config=config)\n",
    "results_cobrapy, _ = biosimulators_cobrapy.exec_sedml_docs_in_combine_archive(archive_filename, output_dirname, config=config)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9de107c5-4012-4d57-9844-a13d5e76ad26",
   "metadata": {},
   "source": [
    "Check that the predicted objectives are positive"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "id": "a4e20ad9-97c7-45fa-a219-d495b573cccb",
   "metadata": {},
   "outputs": [],
   "source": [
    "assert results_cbmpy['simulation.sedml']['objective']['obj'] > 0\n",
    "assert results_cobrapy['simulation.sedml']['objective']['obj'] > 0"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ab055a95-ea84-4540-947f-1d94ad006267",
   "metadata": {},
   "source": [
    "Check that the simulators produced consistent objective values"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "id": "18b1543b-37ad-4e3e-8572-a3d6f7037de8",
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy.testing"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "id": "73742eea-53b4-42d4-b9cd-92766aa4c0a9",
   "metadata": {},
   "outputs": [],
   "source": [
    "numpy.testing.assert_allclose(\n",
    "    results_cbmpy['simulation.sedml']['objective']['obj'],\n",
    "    results_cobrapy['simulation.sedml']['objective']['obj'],\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "cf5774fa-c87c-4a65-8f89-402a1a41def3",
   "metadata": {},
   "source": [
    "### 3.17. Submit model to runBioSimulations"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "df53667d-c262-4be8-ae20-d120f2ff1cd1",
   "metadata": {
    "tags": []
   },
   "source": [
    "The following code can be used to submit the COMBINE/OMEX archive to runBioSimulations."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "id": "98e47164-faab-48c9-a73b-88146f767994",
   "metadata": {},
   "outputs": [],
   "source": [
    "from biosimulators_utils.biosimulations.utils import run_simulation_project"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "id": "673d5653-eefa-4f54-ad9e-0cdf48e671aa",
   "metadata": {},
   "outputs": [],
   "source": [
    "run_id = run_simulation_project(\n",
    "    name=metadata['title'], \n",
    "    filename_or_url=archive_filename, \n",
    "    simulator='cobrapy')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "id": "eeb08b2b-5681-4fad-a46d-547870695a0b",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "https://run.biosimulations.org/simulations/61ba2c799ecb3476cd34c1d9\n"
     ]
    }
   ],
   "source": [
    "print('https://run.biosimulations.org/simulations/' + run_id)"
   ]
  }
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