biosimulators-rbapy 0.0.4

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

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).