Installation instructions

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

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.

Command-line program

First, install Python, Pip, and optionally IBM CPLEX.

Second, run the following command to install BioSimulators-RBApy:

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]

Docker image with a command-line entrypoint

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

docker pull ghcr.io/biosimulators/rbapy