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:
2023-04-12