From 166083b3c3d78af547d1f2969d8ff1ff5ebe3188 Mon Sep 17 00:00:00 2001 From: biosimulatorsdaemon Date: Sun, 29 Aug 2021 16:19:33 +0000 Subject: [PATCH] Updating compiled documentation --- docs/_static/documentation_options.js | 2 +- docs/about.html | 21 +++++++++-------- docs/genindex.html | 2 +- docs/index.html | 13 ++++++----- docs/installation.html | 17 +++++++------- docs/py-modindex.html | 2 +- docs/search.html | 2 +- docs/source/biosimulators_ginsim.html | 25 ++++++++++---------- docs/tutorial.html | 33 ++++++++++++++------------- 9 files changed, 61 insertions(+), 56 deletions(-) diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js index 4bfda28..1f7a801 100644 --- a/docs/_static/documentation_options.js +++ b/docs/_static/documentation_options.js @@ -1,6 +1,6 @@ var DOCUMENTATION_OPTIONS = { URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), - VERSION: '0.0.4', + VERSION: '0.0.5', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/docs/about.html b/docs/about.html index 860ae24..228c103 100644 --- a/docs/about.html +++ b/docs/about.html @@ -4,8 +4,9 @@ - - About BioSimulators-GINsim — BioSimulators-GINsim 0.0.4 documentation + + + About BioSimulators-GINsim — BioSimulators-GINsim 0.0.5 documentation @@ -112,21 +113,21 @@

Quick search

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About BioSimulators-GINsim

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License

This package is released under the MIT License. GINsim is released under the GPL 3.0 License.

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Development team

This package was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai and the Center for Reproducible Biomedical Modeling. GINsim was developed at the Gulbenkian Institute of Science.

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Questions and comments

Please contact the BioSimulators Team with any questions or comments about the command-line program or Docker image. Please contact the GINsim Team with any questions or comments about GINsim.

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Quick search

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BioSimulators-GINsim documentation

BioSimulators-GINsim provides a BioSimulators-compliant command-line interface to the GINsim biological simulation tool. A Docker image for this package is also available.

This command-line interface and Docker image enable users to use GINsim to execute COMBINE/OMEX archives that describe one or more simulation experiments (in SED-ML format) of one or more logical models (in SBML-qual format).

A list of the algorithms and algorithm parameters supported by GINsim is available at BioSimulators.

A simple web application and web service for using GINsim to execute COMBINE/OMEX archives is also available at runBioSimulations.

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Contents

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    ContentsIndex

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diff --git a/docs/installation.html b/docs/installation.html index 2e1da9f..8cd482e 100644 --- a/docs/installation.html +++ b/docs/installation.html @@ -4,8 +4,9 @@ - - Installation instructions — BioSimulators-GINsim 0.0.4 documentation + + + Installation instructions — BioSimulators-GINsim 0.0.5 documentation @@ -111,24 +112,24 @@

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Installation instructions

BioSimulators-GINsim is available as a command-line program and as a command-line program encapsulated into a Docker image.

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Command-line program

After installing the Java, Python (>= 3.7),`pip <https://pip.pypa.io/>`_, and the GINsim Python API, run the following command to install BioSimulators-GINsim:

pip install biosimulators-ginsim
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Docker image with a command-line entrypoint

After installing Docker, run the following command to install the Docker image for BioSimulators-GINsim:

docker pull ghcr.io/biosimulators/ginsim
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biosimulators_ginsim package

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Submodules

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biosimulators_ginsim.core module

BioSimulators-compliant command-line interface to the GINsim simulation program.

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biosimulators_ginsim.data_model module

Data model

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biosimulators_ginsim.utils module

Utility methods

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Submodules - - Tutorial — BioSimulators-GINsim 0.0.4 documentation + + + Tutorial — BioSimulators-GINsim 0.0.5 documentation @@ -112,27 +113,27 @@

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Tutorial

BioSimulators-GINsim is available as a command-line program and as a command-line program encapsulated into a Docker image.

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Creating COMBINE/OMEX archives and encoding simulation experiments into SED-ML

Information about how to create COMBINE/OMEX archives which can be executed by BioSimulators-GINsim is available at BioSimulators.

A list of the algorithms and algorithm parameters supported by GINsim is available at BioSimulators.

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Models (SBML-qual)

BioSimulators-GINsim can execute models encoded in the qual package of SBML and GINsim’s format (zginml).

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Simulation experiments (SED-ML, KISAO)

BioSimulators-GINsim can execute simulation experiments encoded in SED-ML, using KiSAO to indicate specific algorithms and their parameters. Information about the algorithms (KiSAO terms), algorithm parameters (KiSAO terms), and outputs (XML XPaths for variables) supported by BioSimulators-GINsim is available from the BioSimulators registry.

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Example COMBINE/OMEX archives

Examples of COMBINE/OMEX archives for logical simulations which BioSimulators-GINsim can execute are available in the BioSimulators test suite.

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Command-line program

The command-line program can be used to execute COMBINE/OMEX archives that describe simulations as illustrated below.

usage: biosimulators-ginsim [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]
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Command-line program
biosimulators-ginsim -i ./modeling-study.omex -o ./
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Docker image with a command-line entrypoint

The entrypoint to the Docker image supports the same command-line interface described above.

For example, the following command could be used to use the Docker image to execute the same simulations described in ./modeling-study.omex and save their results to ./:

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Docker image with a command-line entrypoint