Repositories list

• biosimulations

  Public
  A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results

  simulationbiologymodeling+ 9

  simulationbiologymodelingbiological-simulationsstandardsvegareproducibilitybiosimulationsbmlsed-ml+ 2

  TypeScript

  •

  MIT License

  •1616 forks•4343 stars•114114 issues•2121 pull requests•Updated Aug 2, 2026Aug 2, 2026

• status

  Public
  📈 Uptime monitor and status page for BioSimulations, powered by @upptime

  uptime-monitorstatus-pageupptime

  uptime-monitorstatus-pageupptime

  Markdown

  •

  MIT License

  •11 fork•00 stars•22 issues•00 pull requests•Updated Aug 2, 2026Aug 2, 2026

• compose-api

  Public
  An API server for reproducible biological workflows and cosimulations.

  Python

  •

  MIT License

  •00 forks•00 stars•2323 issues•2323 pull requests•Updated Aug 1, 2026Aug 1, 2026

• platform

  Public
  Server for the Biological Simulation Verification Service (BSVS)

  Python

  •

  MIT License

  •11 fork•11 star•22 issues•2626 pull requests•Updated Jul 31, 2026Jul 31, 2026

• biosim-client

  Public
  library for accessing biosimulations APIs.

  Python

  •

  MIT License

  •00 forks•00 stars•99 issues•1111 pull requests•Updated Jul 31, 2026Jul 31, 2026

• deployment

  Public
  Kubernetes Configuration for BioSimulations

  kubernetesargogitops+ 2

  kubernetesargogitopsargocdbiosimulations

  Shell

  •

  MIT License

  •11 fork•33 stars•66 issues•55 pull requests•Updated Jul 30, 2026Jul 30, 2026

• .github

  Public
  GitHub profile for the BioSimulations organization

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 30, 2026Jul 30, 2026

• sed

  Public
  All Python related code related to the new SED standard.

  Python

  •

  Apache License 2.0

  •00 forks•11 star•66 issues•99 pull requests•Updated Jul 28, 2026Jul 28, 2026

• biosimulations-modeldb

  Public
  Command-line program and scheduled GitHub action for publishing the ModelDB model repository to BioSimulations

  systems-biologycomputational-biologyelectrophysiology+ 7

  systems-biologycomputational-biologyelectrophysiologyneuroncombinemodeldbxppsed-mlomexbiosimulations

  MATLAB

  •

  MIT License

  •00 forks•00 stars•22 issues•55 pull requests•Updated Jul 25, 2026Jul 25, 2026

• biosimulations-bigg

  Public
  Command-line program and scheduled GitHub action for publishing the BiGG model repository to BioSimulations

  systems-biologycomputational-biologymetabolism+ 10

  systems-biologycomputational-biologymetabolismcombinesbmlflux-balance-analysisfbacell-biologysed-mlomex+ 3

  Python

  •

  MIT License

  •00 forks•11 star•33 issues•55 pull requests•Updated Jul 25, 2026Jul 25, 2026

• biomodels-regression

  Public
  Python

  •00 forks•00 stars•00 issues•88 pull requests•Updated Jul 22, 2026Jul 22, 2026

• pbsim_common

  Public
  A repository filled with high quality processes, steps, and composites for process bi-graph. All used as a standard library for process bi-graph.

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•1212 pull requests•Updated Jul 21, 2026Jul 21, 2026

• biosimulations-runutils

  Public
  Automation tools for running and comparing biosimulations from OMEX archives.

  Python

  •

  MIT License

  •00 forks•00 stars•11 issue•33 pull requests•Updated Jul 3, 2026Jul 3, 2026

• compose-api-client

  Public
  Generated clients for the compose API.

  Python

  •00 forks•00 stars•00 issues•44 pull requests•Updated May 19, 2026May 19, 2026

• pbest

  Public
  The Process Bi-Graph Extensible Simulation Toolkit is a Python-based tool for creating and executing Process Bi-Graphs, either locally or remotely.

  Python

  •

  Apache License 2.0

  •00 forks•00 stars•44 issues•1010 pull requests•Updated May 15, 2026May 15, 2026

• registry

  Public
  Registry of all supported repositories that have PBG wrappers.

  MIT License

  •00 forks•00 stars•00 issues•11 pull request•Updated May 9, 2026May 9, 2026

• pbsim_actin

  Public
  Multiscale-actin Wrapper for PBG

  Python

  •

  Apache License 2.0

  •00 forks•00 stars•77 issues•11 pull request•Updated Apr 22, 2026Apr 22, 2026

• process-bigraph-lang

  Public
  Domain Specific Language and Language Server for Process Bigraphs

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•1414 pull requests•Updated Feb 14, 2026Feb 14, 2026

• biomodels-qc

  Public
  Quality control tool for the BioModels repository of biochemical models

  testingquality-controlvalidation+ 4

  testingquality-controlvalidationsystems-biologycomputational-modelbiomodelsnumerical-simulation

  Python

  •

  MIT License

  •00 forks•00 stars•11 issue•00 pull requests•Updated May 21, 2025May 21, 2025

• eslint-plugin-exclude-strings

  Public
  TypeScript

  •00 forks•00 stars•00 issues•77 pull requests•Updated Dec 15, 2023Dec 15, 2023

• static

  Public
  Repository for holding static files hosted at https://static.biosimulations.org

  CSS

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 15, 2023Dec 15, 2023

• hsds

  Public
  Cloud-native, service based access to HDF data

  Python

  •

  Apache License 2.0

  •6060 forks•00 stars•00 issues•00 pull requests•Updated Apr 4, 2023Apr 4, 2023

• nestjs-bullmq

  Public
  TypeScript

  •

  MIT License

  •1111 forks•00 stars•11 issue•11 pull request•Updated Apr 4, 2023Apr 4, 2023

• material-file-input

  Public
  File input for Angular Material form-field

  TypeScript

  •

  MIT License

  •6464 forks•00 stars•00 issues•00 pull requests•Updated Apr 4, 2023Apr 4, 2023

• nx-python

  Public
  🐍 Plugin for using Python in an Nx Workspace

  TypeScript

  •

  MIT License

  •1010 forks•00 stars•00 issues•00 pull requests•Updated Apr 4, 2023Apr 4, 2023

• hdf-rest-api

  Public
  Python

  •55 forks•00 stars•00 issues•00 pull requests•Updated Apr 4, 2023Apr 4, 2023

• biosimulations-rulehub

  Public
  Repository of rule-based models implemented with the BioNetGen model language (BNGL) and command-line program for publishing RuleHub to BioSimulations

  systems-biologycomputational-biologycombine+ 6

  systems-biologycomputational-biologycombinebionetgensed-mlomexbiosimulationsrulehubbngl

  Python

  •

  MIT License

  •77 forks•11 star•00 issues•00 pull requests•Updated Apr 4, 2023Apr 4, 2023

• cellml-validation

  Public
  A suite of CellML files used to test validation methods

  Python

  •

  Other

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 3, 2023Apr 3, 2023

• biosimulations-physiome

  Public
  Command-line application for publishing the Physiome model repository of physiological models to the BioSimulations repository for simulation projects

  systems-biologycomputational-biologycombine+ 5

  systems-biologycomputational-biologycombinepmrcellmlsed-mlomexphysiome-model-repository

  JavaScript

  •00 forks•00 stars•77 issues•00 pull requests•Updated May 16, 2022May 16, 2022

• Owl2Json

  Public
  A very simple Java program to produce a JSON file from an ontology IRI

  Java

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 4, 2021Oct 4, 2021