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    108 repositories

    • PaperSummaryDataset

      Public
      A workflow for generating summaries of research papers on biological models using generative AI.
      Python
      •
      MIT License
      •0•0•0•1•Updated Nov 12, 2024Nov 12, 2024

    • 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
      •2•0•1•0•Updated Nov 12, 2024Nov 12, 2024

    • AntimonyEditor

      Public
      Antimony Web Editor: A Web Editor for the Antimony Modeling Language
      TypeScript
      •
      MIT License
      •1•0•18•2•Updated Nov 12, 2024Nov 12, 2024

    • antimony

      Public
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •4•16•25•1•Updated Nov 8, 2024Nov 8, 2024

    • libroadrunner-deps

      Public
      Dependencies for libroadrunner
      CMake
      •5•3•0•0•Updated Nov 8, 2024Nov 8, 2024

    • SimBioUI

      Public
      Web systems biology simulator
      JavaScript
      •
      MIT License
      •2•0•3•0•Updated Nov 8, 2024Nov 8, 2024

    • evolution

      Public
      Tool used to create oscillatory networks. Generates reaction network models in Antimony, which can be easily converted to SBML (SBML.org) for further analysis. This is the main repository for Evolution, superseding the original one at https://github.com/ltatka/evolution.
      C
      •
      MIT License
      •0•0•0•0•Updated Nov 6, 2024Nov 6, 2024

    • OcillatorDatabase

      Public
      Database of oscillatory chemical network models. Written in Antimony.
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 4, 2024Nov 4, 2024

    • BiomodelsStore

      Public
      JavaScript
      •2•0•0•0•Updated Nov 4, 2024Nov 4, 2024

    • BiomodelsCache

      Public
      A biomodels cache for faster lookup.
      Python
      •
      Creative Commons Zero v1.0 Universal
      •1•0•0•0•Updated Nov 1, 2024Nov 1, 2024

    • roadrunner

      Public
      libRoadRunner: A high-performance SBML simulator
      sbmlsbml-simulation
      C++
      •
      Other
      •33•39•71•2•Updated Oct 24, 2024Oct 24, 2024

    • ratesb_python

      Public
      Analysis of rate laws in reaction networks.
      Python
      •
      MIT License
      •0•0•5•0•Updated Oct 14, 2024Oct 14, 2024

    • nleq2

      Public
      C
      •0•0•0•0•Updated Oct 12, 2024Oct 12, 2024

    • zlib

      Public
      A massively spiffy yet delicately unobtrusive compression library.
      C
      •2.5k•0•0•0•Updated Sep 17, 2024Sep 17, 2024

    • libxml2

      Public
      C
      •
      Other
      •0•1•0•0•Updated Sep 17, 2024Sep 17, 2024

    • libxslt

      Public
      Read-only mirror of https://gitlab.gnome.org/GNOME/libxslt
      HTML
      •
      Other
      •44•0•0•0•Updated Sep 17, 2024Sep 17, 2024

    • iconv

      Public
      C
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 17, 2024Sep 17, 2024

    • temp-biomodels

      Public
      Temporary place for coordination of updating existing Biomodels
      Component Pascal
      •
      Creative Commons Zero v1.0 Universal
      •2•2•13•0•Updated Aug 27, 2024Aug 27, 2024

    • makesbml

      Public
      Simple site to convert antimony to sbml
      systems-biologysbml-models
      JavaScript
      •
      Apache License 2.0
      •1•1•1•1•Updated Aug 24, 2024Aug 24, 2024

    • InteractiveModels

      Public
      Models and simulator for Interactive modeling site: https://sites.google.com/view/interactive-modeling/home
      JavaScript
      •
      Apache License 2.0
      •0•1•0•0•Updated Aug 23, 2024Aug 23, 2024

    • 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
      •12k•0•0•1•Updated Aug 15, 2024Aug 15, 2024

    • rr-libstruct

      Public
      C++
      •1•1•0•0•Updated Aug 15, 2024Aug 15, 2024

    • libantimonyjs

      Public
      JavaScript version of the antimony library to support human-readable, human-writable modular model definition language.
      JavaScript
      •0•1•2•0•Updated Jul 21, 2024Jul 21, 2024

    • artificial_random_signaling_network

      Public
      Julia
      •
      MIT License
      •1•0•0•0•Updated Jul 20, 2024Jul 20, 2024

    • pyPESTO

      Public
      python Parameter EStimation TOolbox
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •47•0•0•0•Updated Jul 17, 2024Jul 17, 2024

    • EGFR

      Public
      Python
      •0•0•0•0•Updated Jul 9, 2024Jul 9, 2024

    • ReactionNetworkEvolution.jl

      Public
      A configurable reaction network evolver
      Julia
      •
      MIT License
      •1•0•0•1•Updated Jun 26, 2024Jun 26, 2024

    • Developing-a-workflow-for-creating-OMEX-files

      Public
      Component Pascal
      •
      MIT License
      •1•0•0•0•Updated Jun 24, 2024Jun 24, 2024

    • phrasedml

      Public
      Git mirror of https://sourceforge.net/projects/phrasedml/
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated Jun 24, 2024Jun 24, 2024

    • frequencyResponse

      Public
      Computes frequency response for a SBML model
      Python
      •
      MIT License
      •0•1•0•0•Updated Jun 16, 2024Jun 16, 2024