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|
|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|