BioSimulators-RBApy

BioSimulators-compliant command-line interface to the RBApy simulation program for Resource Balance Analysis (RBA) models.

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

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

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

Installation

BioSimulators-RBApy requires one of the linear programming solvers IBM CPLEX, GLPK, or Gurobi. Note, GLPK is slower than CPLEX and Gurobi. IBM and Gurobi both provide free licenses for academic research.

Install Python package

1. Install requirements

   • Python
   • Pip
   • Optionally, install CPLEX

2. Install this package

   pip install biosimulators-rbapy
   

   To use BioSimulators-RBApy with CPLEX, install BioSimulators-RBApy with the cplex option. Note, this requires CPLEX and a CPLEX license:

   pip install rbapy[cplex]
   

   To use BioSimulators-RBApy with GLPK, install BioSimulators-RBApy with the glpk option. Note, this requires libglpk-dev:

   pip install rbapy[glpk]
   

   To use BioSimulators-RBApy with Gurobi, install BioSimulators-RBApy with the gurobi option. Note, this requires a Gurobi license:

   pip install rbapy[gurobi]
   

Install Docker image

docker pull ghcr.io/biosimulators/rbapy

Usage

Local usage

usage: biosimulators-rbapy [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the RBApy simulation program <https://sysbioinra.github.io/RBApy/>.

optional arguments:
  -h, --help            show this help message and exit
  -d, --debug           full application debug mode
  -q, --quiet           suppress all console output
  -i ARCHIVE, --archive ARCHIVE
                        Path to OMEX file which contains one or more SED-ML-
                        encoded simulation experiments
  -o OUT_DIR, --out-dir OUT_DIR
                        Directory to save outputs
  -v, --version         show program's version number and exit

Usage through Docker container

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 COMBINE/OMEX archive ./modeling-study.omex and save its outputs to ./.

docker run \
  --tty \
  --rm \
  --mount type=bind,source="$(pwd)",target=/root/in,readonly \
  --mount type=bind,source="$(pwd)",target=/root/out \
  ghcr.io/biosimulators/rbapy:latest \
    -i /root/in/modeling-study.omex \
    -o /root/out

Using BioSimulators-RBApy with a Gurobi license

Gurobi licenses can be used either by setting environment variables prefixed with GRB_ or by saving your license to your home directory (~/gurobi.lic) or the appropriate location for your OS (e.g., /opt/gurobi/gurobi.lic for Linux).

Documentation

Documentation is available at https://docs.biosimulators.org/Biosimulators_RBApy/.

License

This package is released under the MIT license.

Development team

This package was developed by the Center for Reproducible Biomedical Modeling and the Karr Lab at the Icahn School of Medicine at Mount Sinai in New York with assistance from the contributors listed here.

Questions and comments

Please contact the BioSimulators Team with any questions or comments.