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]

Dockerfile and Docker image#

This package is available in the ghcr.io/biosimulators/biosimulators Docker image. This image includes all of the optional dependencies and installation options.

To install and run this image, run the following commands:

docker pull ghcr.io/biosimulators/biosimulators
docker run -it --rm ghcr.io/biosimulators/biosimulators

This image includes this package, as well as standardized Python APIs for the simulation tools validated by BioSimulators. Because this image aims to incorporate as many simulation tools as possible within a single Python environment, this image may sometimes lag behind the latest version of this package.

The Dockerfile for this image is available here.