https://github.com/biosimulators/Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface

combine computational-biology docker kinetic-model kisao mathematical-model omex reproducibility reuse sbml sbo sed-ml simulation systems-biology

Last synced: 14 Oct 2025

https://github.com/biosimulators/biosimulators_simulator_template

Template for a repository for building a BioSimulators-compliant command-line interface and Dockerfile for a biosimulation program

biosimulators combine-archive computational-biology docker mathematical-modelling omex-metadata python sed-ml simulation simulator systems-biology

Last synced: 12 Feb 2026

https://github.com/biosimulators/biosimulators_tutorials

Tutorials for BioSimulators

biosimulations biosimulators combine computational-biology jupyter mathematical-modeling numerical-simulation omex sbml sed-ml systems-biology tutorial

Last synced: 12 Feb 2026

https://github.com/biosimulators/biosimulators_copasi

COPASI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

biochemical-networks biosimulators combine-archive computational-biology copasi docker dynamical-modeling omex-metadata python sbml sed-ml simulation systems-biology

Last synced: 14 Jan 2026

https://github.com/biosimulators/biosimulators.github.io

Summary of the technical documentation for BioSimulators

biosimulators combine computational-biology modeling omex sbml sed-ml simulation systems-biology

Last synced: 12 Feb 2026

https://github.com/biosimulators/compose-server

This repo is intended to replace both the bio-check and bio-compose-server repos. The aforementioned repos will be archived.

Last synced: 12 Feb 2026

https://github.com/biosimulators/bspil-basico

BioSimulators Process Interface Library for COPASI through the Basico python wrapper

Last synced: 12 Feb 2026

https://github.com/biosimulators/bsvs

A high-level Python client for the Biological Simulation Verification Service REST API.

Last synced: 12 Feb 2026

https://github.com/biosimulators/bsander

Analyzes a Process-Bigraph `.pbif` file, and creates a configuration that will run in a given environment.

Last synced: 12 Feb 2026

https://github.com/biosimulators/bsew

Wrapper package from running Process Bigraph experiments in a docker environment

Last synced: 12 Feb 2026

https://github.com/biosimulators/.github

Profile for the BioSimulators organization

Last synced: 12 Feb 2026