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    23 repositories

    • nfsim

      Public
      A general-purpose, stochastic, biochemical reaction simulator for large reaction networks
      C++
      •
      MIT License
      •19•14•14•1•Updated Aug 28, 2025Aug 28, 2025

    • webng

      Public
      A set of tools to simplify the weighted ensemble sampling of BioNetGen rule-based simulations.
      Jupyter Notebook
      •
      Other
      •4•0•5•0•Updated Jun 17, 2025Jun 17, 2025

    • bionetgen

      Public
      Rule-based modeling framework
      Perl
      •
      MIT License
      •24•65•66•3•Updated May 28, 2025May 28, 2025

    • PyBioNetGen

      Public
      A simple CLI for BioNetGen
      Python
      •
      MIT License
      •4•5•11•0•Updated Apr 24, 2025Apr 24, 2025

    • BNGTutorial

      Public
      Models that demonstrate the syntax and functionality of BioNetGen language and simulation tools.
      3•15•0•0•Updated May 30, 2023May 30, 2023

    • BNG_vscode_extension

      Public
      JavaScript
      •
      MIT License
      •2•4•6•0•Updated Apr 20, 2023Apr 20, 2023

    • atomizer

      Public
      RNM to RBM translation project.
      Python
      •5•3•2•7•Updated Jul 6, 2022Jul 6, 2022

    • RuleHub

      Public
      A repository of rule-based models. Could this be the start of something great?
      Python
      •
      MIT License
      •3•1•0•0•Updated Sep 19, 2021Sep 19, 2021

    • ptempest

      Public
      PTempEst: Parallel Tempering for Estimation
      MATLAB
      •
      GNU General Public License v3.0
      •5•5•0•0•Updated Oct 27, 2020Oct 27, 2020

    • SupplementalMaterials

      Public
      Repository for supplemental materials of published papers related to RuleWorld projects.
      MATLAB
      •0•0•0•0•Updated Aug 5, 2020Aug 5, 2020

    • rulebender

      Public
      Rule-Based Modeling and Simulation Gui
      C
      •7•12•65•0•Updated Jun 12, 2020Jun 12, 2020

    • BNGParser

      Public
      GAP
      •1•0•0•1•Updated May 15, 2019May 15, 2019

    • TRuML

      Public
      Python
      •
      Other
      •4•0•0•0•Updated Feb 26, 2019Feb 26, 2019

    • RuleBuilder

      Public
      A tool for graphical construction and visualization of BioNetGen graphs
      Java
      •
      Other
      •2•0•0•0•Updated Feb 26, 2019Feb 26, 2019

    • BioNetFit

      Public
      An application for fitting BioNetGen models using a genetic algorithm
      Perl
      •
      GNU General Public License v3.0
      •3•1•1•0•Updated Dec 12, 2018Dec 12, 2018

    • mcellRules

      Public
      Jupyter Notebook
      •3•1•1•0•Updated Aug 21, 2018Aug 21, 2018

    • RulebenderOnline

      Public
      JavaScript
      •0•1•0•0•Updated May 8, 2018May 8, 2018

    • PhiBPlot

      Public
      0•0•0•0•Updated Feb 13, 2018Feb 13, 2018

    • RB-website

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Jan 12, 2018Jan 12, 2018

    • atomizer_testing

      Public
      Testing files for atomizer
      Component Pascal
      •1•0•0•0•Updated Nov 5, 2017Nov 5, 2017

    • ratomizer

      Public
      Atomizer webapp
      Python
      •0•0•0•0•Updated Aug 17, 2016Aug 17, 2016

    • nfsimCInterface

      Public
      A C interface for the NFSim API
      C++
      •2•1•0•0•Updated Jul 1, 2016Jul 1, 2016

    • rulehub-server

      Public
      A database portal for rule-based models
      Python
      •0•0•0•0•Updated Apr 24, 2015Apr 24, 2015