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Documentation for libraries for publishing primary model repositories to BioSimulations

A portion of BioSimulations is derived from several primary model repositories that focus on models of specific biological systems, specific types of models, specific model formats, and/or specific simulation tools. We aim to automatically publish these repositories to BioSimulations each week. This publication will be implemented by a collection of Python packages and GitHub actions. Links to documentation for these packages will be available below.

Repository Topic Formalism Format Tools Docs for publication to BioSimulations
BiGG Metabolism Flux balance SBML-fbc COBRApy and others Docs
BioModels Biochemical networks Kinetic SBML Many
GINsim Networks Qualitative ZGINML GINsim
ModelDB Neurophysiology Continuous kinetic ODE and others XPP and others
Physiome Physiology Continuous kinetic CellML OpenCOR and others
RBA models Resource allocation Resource balance RBA XML RBAPy
Rule Hub Rule-based models Discrete kinetic BNGL BioNetGen

Last update: 2022-07-03