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@sys-bio UW Sauro Lab

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    118 repositories

    • BiomodelsStore

      Public
      JavaScript
      •1•0•0•0•Updated Jan 1, 2026Jan 1, 2026

    • cesium

      Public
      Database of Oscillatory and random chemical network models written in Antimony format.
      Python
      •1•0•0•0•Updated Jan 1, 2026Jan 1, 2026

    • 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•3•7•0•Updated Dec 25, 2025Dec 25, 2025

    • roadrunner

      Public
      libRoadRunner: A high-performance SBML simulator
      sbmlsbml-simulation
      C++
      •
      Other
      •36•55•74•3•Updated Dec 20, 2025Dec 20, 2025

    • AAAIM

      Public
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Dec 18, 2025Dec 18, 2025

    • WebIridium

      Public
      Web-based simulation and analysis of biological models
      TypeScript
      •1•2•12•2•Updated Dec 14, 2025Dec 14, 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 Dec 5, 2025Dec 5, 2025

    • tellurium

      Public
      Python Environment for Modeling and Simulating Biological Systems
      Python
      •
      Apache License 2.0
      •40•130•128•4•Updated Dec 5, 2025Dec 5, 2025

    • BMCA-evals

      Public
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Dec 2, 2025Dec 2, 2025

    • libroadrunner-deps

      Public
      Dependencies for libroadrunner
      CMake
      •5•3•0•2•Updated Nov 26, 2025Nov 26, 2025

    • poco

      Public
      The POCO C++ Libraries are powerful cross-platform C++ libraries for building network- and internet-based applications that run on desktop, server, mobile, IoT, and embedded systems.
      C++
      •
      Other
      •2.3k•0•0•0•Updated Nov 26, 2025Nov 26, 2025

    • antimony

      Public
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •4•19•19•0•Updated Nov 21, 2025Nov 21, 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 Nov 21, 2025Nov 21, 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
      •16k•0•0•0•Updated Oct 31, 2025Oct 31, 2025

    • libStochastic

      Public
      A portable C based library that implements the Gillespie direct method.
      C++
      •
      Apache License 2.0
      •0•0•0•0•Updated Oct 28, 2025Oct 28, 2025

    • Alcuin2

      Public
      Biochemical Network Visualization and Editor
      MIT License
      •0•0•0•0•Updated Oct 19, 2025Oct 19, 2025

    • TabularQual

      Public
      Python
      •
      MIT License
      •1•5•2•0•Updated Oct 10, 2025Oct 10, 2025

    • ratesb_python

      Public
      Analysis of rate laws in reaction networks.
      Python
      •
      MIT License
      •2•1•8•0•Updated Oct 9, 2025Oct 9, 2025

    • AntimonyEditor

      Public
      Antimony Web Editor: A Web Editor for the Antimony Modeling Language
      TypeScript
      •
      MIT License
      •2•0•22•1•Updated Sep 30, 2025Sep 30, 2025

    • EGFR_reference_models

      Public
      Jupyter Notebook
      •0•0•2•0•Updated Sep 22, 2025Sep 22, 2025

    • SimBioUI

      Public
      Web systems biology simulator
      JavaScript
      •
      MIT License
      •2•0•13•0•Updated Aug 22, 2025Aug 22, 2025

    • SBMLNetworkWeb

      Public
      A web implementation of SBMLNetwork
      HTML
      •1•0•0•0•Updated Aug 7, 2025Aug 7, 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

    • rr-libstruct

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

    • BestPractices_KineticModels

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