Installation instructions

Requirements

  • Python >= 3.7

  • pip

Optional requirements

  • Docker: required to execute containerized simulation tools

  • Java: required to parse and validate NeuroML/LEMS files

  • Perl: required to parse and validate BioNetGen files

  • RBApy: required to parse and validate RBA files

  • XPP: required to parse and validate XPP files

Installing the latest release from PyPI

After installing Python (>= 3.7) and pip, run the following command to install BioSimulators utils:

pip install biosimulators-utils

Installing the latest revision from GitHub

After installing Python (>= 3.7) and pip, run the following command to install BioSimulators utils:

pip install git+https://github.com/biosimulators/Biosimulators_utils#egg=biosimulators_utils

Installing the optional features

To use BioSimulators utils to validate models encoded in BNGL, install BioSimulators utils with the bngl option:

pip install biosimulators-utils[bngl]

To use BioSimulators utils to validate models encoded in CellML, install BioSimulators utils with the cellml option:

pip install biosimulators-utils[cellml]

To use BioSimulators utils to validate models encoded in LEMS, install Java and then install BioSimulators utils with the lems option:

pip install biosimulators-utils[lems]

To use BioSimulators utils to validate models encoded in NeuroML, install BioSimulators utils with the neuroml option:

pip install biosimulators-utils[neuroml]

To use BioSimulators utils to validate models encoded in SBML, install BioSimulators utils with the sbml option:

pip install biosimulators-utils[sbml]

To use BioSimulators utils to validate models encoded in Smoldyn, install BioSimulators utils with the smoldyn option:

pip install biosimulators-utils[smoldyn]

To use BioSimulators utils to convert Escher metabolic maps to Vega flux data visualizations, install BioSimulators utils with the escher option:

pip install biosimulators-utils[escher]

To use BioSimulators utils to execute containerized simulation tools, install BioSimulators utils with the containers option:

pip install biosimulators-utils[containers]

To use BioSimulators utils to log the standard output and error produced by simulation tools, install BioSimulators utils with the logging option:

pip install biosimulators-utils[logging]