Package: biosimulators-rbapy
BioSimulators-RBApyBioSimulators-compliant command-line interface to theRBApysimulation program for
Resource Balance Analysis (RBA) models.This command-line interface and Docker image enable users to use RBApy
to executeCOMBINE/OMEX archivesthat
describe one or more simulation experiments (inSED-ML
format) of one or more RBA models in theRBApy
format.A list of the algorithms and algorithm parameters supported by RBApy is
available atBioSimulators.A simple web application and web service for using RBApy to execute
COMBINE/OMEX archives is also available atrunBioSimulations.InstallationBioSimulators-RBApy requires one of the linear programming solversIBM
CPLEX,GLPK, orGurobi. Note,
GLPK is slower than CPLEX and Gurobi. IBM and Gurobi both provide free
licenses for academic research.Install Python packageInstall requirementsPythonPipOptionally, install CPLEXInstall this packagepip install biosimulators-rbapyTo use BioSimulators-RBApy with CPLEX, install BioSimulators-RBApy
with thecplexoption. Note, this requires CPLEX and a CPLEX
license:pip install rbapy[cplex]To use BioSimulators-RBApy with GLPK, install BioSimulators-RBApy
with theglpkoption. Note, this requireslibglpk-dev:pip install rbapy[glpk]To use BioSimulators-RBApy with Gurobi, install BioSimulators-RBApy
with thegurobioption. Note, this requires a Gurobi license:pip install rbapy[gurobi]Install Docker imagedocker pull ghcr.io/biosimulators/rbapyUsageLocal usageusage: 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 exitUsage through Docker containerThe 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.omexand 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/outUsing BioSimulators-RBApy with a Gurobi licenseGurobi licenses can be used either by setting environment variables
prefixed withGRB_or by saving your license to your home directory
(~/gurobi.lic) or the appropriate location for your OS (e.g.,/opt/gurobi/gurobi.licfor Linux).DocumentationDocumentation is available athttps://docs.biosimulators.org/Biosimulators_RBApy/.LicenseThis package is released under theMIT license.Development teamThis package was developed by theCenter for Reproducible Biomedical
Modelingand theKarr
Labat the Icahn School of Medicine at
Mount Sinai in New York with assistance from the contributors listedhere.Questions and commentsPlease contact theBioSimulators
Teamwith any questions or comments.