README.md

BioSimulators tutorials

This package provides several tutorials for BioSimulators Python APIs for simulation tools and BioSimulators-utils.

1. Introspecting model/simulation files
   • Extracting the possible inputs and outputs of simulations from model/simulation files
   • Extracting descriptions of simulations and plots from model/simulation files
2. Creating simulation projects
   • Creating SED-ML and COMBINE archives from model files
3. Validating models and simulations
   • Validating models (e.g., CellML, SBML files)
   • Validating simulation experiments (SED-ML files)
   • Validating metadata (OMEX Metadata files)
   • Validating simulation projects (COMBINE-OMEX archives)
4. Finding suitable simulation tools
   • Programmatically getting information about the capabilities of simulation tools (supported model formats, modeling frameworks, simulation types, simulation algorithms) from BioSimulators
5. Executing simulations
   • Executing individual simulations
   • Executing entire simulation projects (COMBINE/OMEX archives that contain one or more models and one or more simulations in SED-ML format)
6. Generating data visualizations for simulation results
   • Converting Escher metabolic flux maps to Vega data visualizations
   • Converting GINsim regulatory network diagrams to Vega data visualizations
   • Converting Systems Biology Graphical Notation (SBGN) Process Description (PD) maps to Vega data visualizations
7. Combining multiple models and/or simulation tools into multi-algorithmic simulations
   • Multi-algorithmic simulation of multiple models and simulation tools

Getting started

Running the tutorials online with Binder

We recommend using the tutorials online through Binder.

Installating the BioSimulators tools

Instructions for installing the BioSimulators simulation tools are available at https://biosimulators.org. A single Docker image with most of the tools is also available (ghcr.io/biosimulators/biosimulators).

Instructions for installing BioSimulators utilities (BioSimulators utils) are available at https://docs.biosimulators.org. BioSimulators utils is also included in the Docker image described above.

Installing a Jupyter server for these tutorials

Instructions for installing a Jupyter server for these tutorials are available at https://github.com/biosimulators/Biosimulators_tutorials. A Docker image is also available (ghcr.io/biosimulators/tutorials).

Reporting bugs

Please help us make BioSimulators great! Please report any issues here.