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    115 repositories

    • SBMLNetwork

      Public
      SBMLNetwork is a library designed to enable software developers and systems biologists to interact with the graphical representation of SBML (Systems Biology Markup Language) models.
      C++
      •
      MIT License
      •1•0•5•0•Updated Aug 9, 2025Aug 9, 2025

    • SimBioUI

      Public
      Web systems biology simulator
      JavaScript
      •
      MIT License
      •2•0•14•0•Updated Aug 8, 2025Aug 8, 2025

    • SBMLNetworkWeb

      Public
      A web implementation of SBMLNetwork
      HTML
      •0•0•0•0•Updated Aug 7, 2025Aug 7, 2025

    • AAAIM

      Public
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Aug 5, 2025Aug 5, 2025

    • AntimonyEditor

      Public
      Antimony Web Editor: A Web Editor for the Antimony Modeling Language
      TypeScript
      •
      MIT License
      •2•0•21•2•Updated Aug 3, 2025Aug 3, 2025

    • WebIridium

      Public
      Web-based simulation and analysis of biological models
      TypeScript
      •0•0•7•0•Updated Aug 1, 2025Aug 1, 2025

    • BiomodelsStore

      Public
      JavaScript
      •1•0•0•0•Updated Aug 1, 2025Aug 1, 2025

    • BiomodelsCache

      Public
      A biomodels cache for faster lookup.
      Python
      •
      Creative Commons Zero v1.0 Universal
      •1•0•0•0•Updated Aug 1, 2025Aug 1, 2025

    • ratesb_python

      Public
      Analysis of rate laws in reaction networks.
      Python
      •
      MIT License
      •2•1•8•1•Updated Jul 25, 2025Jul 25, 2025

    • roadrunner

      Public
      libRoadRunner: A high-performance SBML simulator
      sbmlsbml-simulation
      C++
      •
      Other
      •35•51•77•2•Updated Jul 17, 2025Jul 17, 2025

    • BMCA-pipeline

      Public
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Jul 15, 2025Jul 15, 2025

    • tellurium

      Public
      Python Environment for Modeling and Simulating Biological Systems
      Python
      •
      Apache License 2.0
      •39•122•128•4•Updated Jul 10, 2025Jul 10, 2025

    • antimony

      Public
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •5•18•18•0•Updated Jul 10, 2025Jul 10, 2025

    • rr-libstruct

      Public
      C++
      •1•1•0•0•Updated Jul 9, 2025Jul 9, 2025

    • SimpleSEDML

      Public
      A simple API for using the Simulation Experiment Description Markup Language (SED-ML)
      Jupyter Notebook
      •
      MIT License
      •1•0•2•1•Updated Jul 3, 2025Jul 3, 2025

    • temp-biomodels

      Public
      Temporary place for coordination of updating existing Biomodels
      Component Pascal
      •
      Creative Commons Zero v1.0 Universal
      •2•2•15•0•Updated Jul 1, 2025Jul 1, 2025

    • biomodels_cache

      Public
      Client and admin API for accessing BioModels
      Python
      •
      MIT License
      •1•0•1•1•Updated Jun 27, 2025Jun 27, 2025

    • Antotate

      Public
      Antotate is a tool allowing for the automatic annotation of Antimony files.
      Python
      •
      MIT License
      •1•0•0•0•Updated Jun 12, 2025Jun 12, 2025

    • libantimonyjs

      Public
      JavaScript version of the antimony library to support human-readable, human-writable modular model definition language.
      JavaScript
      •0•1•2•0•Updated Jun 11, 2025Jun 11, 2025

    • BestPractices_KineticModels

      Public
      Best practices in publishing kinetic metabolic models
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Jun 11, 2025Jun 11, 2025

    • cesium

      Public
      Database of Oscillatory and random chemical network models written in Antimony format.
      HTML
      •1•0•0•0•Updated Jun 4, 2025Jun 4, 2025

    • pyomexmeta-binder-notebook

      Public
      About A demonstration of using pyomexmeta - the Python interface to libOmexMeta and the OMEX Metadata Specification.
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated May 20, 2025May 20, 2025

    • libOmexMeta

      Public
      libOmexMeta is a library aimed at providing developer-level support for reading, writing, editing and managing semantic annotations for biosimulation models.
      C
      •
      Apache License 2.0
      •6•8•34•1•Updated May 20, 2025May 20, 2025

    • IridiumSimulator

      Public
      Interactive desktop simulator for systems biology
      Pascal
      •
      MIT License
      •2•3•0•1•Updated May 12, 2025May 12, 2025

    • libroadrunner-deps

      Public
      Dependencies for libroadrunner
      CMake
      •5•4•1•1•Updated May 12, 2025May 12, 2025

    • NuML

      Public
      Numerical Markup Language
      C++
      •8•0•0•0•Updated May 7, 2025May 7, 2025

    • bzip2

      Public
      CMake support for bzip2
      C
      •
      Other
      •8•0•0•0•Updated Apr 14, 2025Apr 14, 2025

    • makesbml

      Public
      Simple site to convert antimony to sbml
      systems-biologysbml-models
      JavaScript
      •
      Apache License 2.0
      •1•1•1•1•Updated Feb 28, 2025Feb 28, 2025

    • PaperSummaryDataset

      Public
      A workflow for generating summaries of research papers on biological models using generative AI.
      Python
      •
      MIT License
      •0•0•0•2•Updated Jan 27, 2025Jan 27, 2025

    • llvm-13.x

      Public
      The LLVM Project is a collection of modular and reusable compiler and toolchain technologies. Note: the repository does not accept github pull requests at this moment. Please submit your patches at http://reviews.llvm.org.
      LLVM
      •15k•0•0•2•Updated Jan 16, 2025Jan 16, 2025