Repositories list

• .github

  Public

  biosimulations/.github’s past year of commit activity
  GitHub profile for the BioSimulations organization

  MIT License

  •0•0•0•0•Updated Mar 13, 2026Mar 13, 2026

• pb_components

  Public

  biosimulations/pb_components’s past year of commit activity
  Monorepo for registry, metadata, and some implementations.

  Python

  •0•0•7•2•Updated Mar 13, 2026Mar 13, 2026

• biosimulations

  Public

  biosimulations/biosimulations’s past year of commit activity
  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

  •16•42•112•16•Updated Mar 13, 2026Mar 13, 2026

• biosim-client

  Public

  biosimulations/biosim-client’s past year of commit activity
  library for accessing biosimulations APIs.

  Python

  •

  MIT License

  •0•0•9•13•Updated Mar 13, 2026Mar 13, 2026

• status

  Public

  biosimulations/status’s past year of commit activity
  📈 Uptime monitor and status page for BioSimulations, powered by @upptime

  uptime-monitorstatus-pageupptime

  uptime-monitorstatus-pageupptime

  Markdown

  •

  MIT License

  •1•0•2•0•Updated Mar 13, 2026Mar 13, 2026

• compose-api

  Public

  biosimulations/compose-api’s past year of commit activity
  An API server for reproducible biological workflows and cosimulations.

  Python

  •

  Other

  •0•0•25•16•Updated Mar 12, 2026Mar 12, 2026

• pbest

  Public

  biosimulations/pbest’s past year of commit activity
  PBest is a BioSimulators project designed to allow users to transform their biological experiments written in Sed into Process-Bigraph simulations.

  Python

  •

  Apache License 2.0

  •0•0•5•7•Updated Mar 12, 2026Mar 12, 2026

• sed

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

  Python

  •

  Apache License 2.0

  •0•1•8•9•Updated Mar 12, 2026Mar 12, 2026

• deployment

  Public

  biosimulations/deployment’s past year of commit activity
  Kubernetes Configuration for BioSimulations

  kubernetesargogitops+ 2

  kubernetesargogitopsargocdbiosimulations

  Shell

  •

  MIT License

  •1•3•6•5•Updated Mar 10, 2026Mar 10, 2026

• biosim-server

  Public

  biosimulations/biosim-server’s past year of commit activity
  Server for the Biological Simulation Verification Service (BSVS)

  Python

  •

  Apache License 2.0

  •0•1•0•28•Updated Mar 3, 2026Mar 3, 2026

• compose-api-client

  Public
  Generated clients for the compose API.

  Python

  •0•0•0•1•Updated Mar 1, 2026Mar 1, 2026

• process-bigraph-lang

  Public
  Domain Specific Language and Language Server for Process Bigraphs

  Python

  •

  MIT License

  •0•0•0•15•Updated Feb 14, 2026Feb 14, 2026

• biosimulations-runutils

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

  Python

  •

  MIT License

  •0•0•1•3•Updated Jan 8, 2026Jan 8, 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

  •0•0•2•5•Updated Dec 12, 2025Dec 12, 2025

• 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

  •0•1•3•5•Updated Dec 11, 2025Dec 11, 2025

• biomodels-qc

  Public
  Quality control tool for the BioModels repository of biochemical models

  testingquality-controlvalidation+ 4

  testingquality-controlvalidationsystems-biologycomputational-modelbiomodelsnumerical-simulation

  Python

  •

  MIT License

  •0•0•1•0•Updated May 21, 2025May 21, 2025

• eslint-plugin-exclude-strings

  Public
  TypeScript

  •0•0•0•7•Updated Dec 15, 2023Dec 15, 2023

• static

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

  CSS

  •

  Apache License 2.0

  •0•0•0•0•Updated Dec 15, 2023Dec 15, 2023

• hsds

  Public
  Cloud-native, service based access to HDF data

  Python

  •

  Apache License 2.0

  •59•0•0•0•Updated Apr 4, 2023Apr 4, 2023

• nestjs-bullmq

  Public
  TypeScript

  •

  MIT License

  •11•0•1•1•Updated Apr 4, 2023Apr 4, 2023

• material-file-input

  Public
  File input for Angular Material form-field

  TypeScript

  •

  MIT License

  •65•0•0•0•Updated Apr 4, 2023Apr 4, 2023

• nx-python

  Public
  🐍 Plugin for using Python in an Nx Workspace

  TypeScript

  •

  MIT License

  •10•0•0•0•Updated Apr 4, 2023Apr 4, 2023

• hdf-rest-api

  Public
  Python

  •5•0•0•0•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

  •3•1•0•0•Updated Apr 4, 2023Apr 4, 2023

• cellml-validation

  Public
  A suite of CellML files used to test validation methods

  Python

  •

  Other

  •1•0•0•0•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

  •0•0•7•0•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

  •0•0•0•0•Updated Oct 4, 2021Oct 4, 2021