Installation instructions¶
Requirements¶
Python >= 3.7
pip
Optional requirements¶
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]