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    39 repositories

    • cellblender

      Public
      Create, Simulate, Visualize, and Analyze Realistic 3D Cell Models
      blendermoleculemcell
      blendermoleculemcell
      Python
      •
      GNU General Public License v2.0
      •16•68•35•2•Updated Apr 15, 2026Apr 15, 2026

    • swift-ir

      Public
      SWiFT-IR: Signal Whitening Fourier Transform Image Registration
      Python
      •
      Mozilla Public License 2.0
      •0•5•1•0•Updated Apr 1, 2026Apr 1, 2026

    • mcell

      Public
      MCell Monte Carlo Simulator of Cellular Microphysiology
      simulationmcellcellblender
      simulationmcellcellblender
      C++
      •
      Other
      •11•38•10•4•Updated Mar 24, 2026Mar 24, 2026

    • mesh_tools

      Public
      A collection of tools for processing and analyzing surface meshes for use with MCell/CellBlender
      mesh
      mesh
      Forth
      •2•6•0•0•Updated Mar 24, 2026Mar 24, 2026

    • mcell_tools

      Public
      Package build repository
      Python
      •
      Other
      •0•2•0•0•Updated Mar 24, 2026Mar 24, 2026

    • gamer

      Public
      Geometry-preserving Adaptive Mesher
      C++
      •
      Other
      •12•0•0•0•Updated Mar 20, 2026Mar 20, 2026

    • neuropil_tools

      Public
      Blender addon to automate annotation and analysis of dendritic spines and axons in neuropil. Requires installation of CellBlender.
      blendermesh
      blendermesh
      Python
      •2•3•9•0•Updated Mar 20, 2026Mar 20, 2026

    • nfsimCInterface

      Public
      A C interface for the NFSim API
      C++
      •
      MIT License
      •2•0•0•0•Updated May 2, 2025May 2, 2025

    • nfsim

      Public
      A general-purpose, stochastic, biochemical reaction simulator for large reaction networks
      C++
      •
      MIT License
      •20•0•0•0•Updated May 2, 2025May 2, 2025

    • mcell_tests

      Public
      New tests for MCell4
      Python
      •
      Other
      •1•2•0•0•Updated May 2, 2025May 2, 2025

    • libbng

      Public
      BioNetGen library
      C++
      •
      Other
      •1•1•0•0•Updated May 2, 2025May 2, 2025

    • bionetgen

      Public
      Rule-based modeling framework
      C
      •
      MIT License
      •26•0•0•0•Updated May 2, 2025May 2, 2025

    • VTK

      Public
      Mirror of Visualization Toolkit repository
      C++
      •
      Other
      •1.3k•0•0•0•Updated May 2, 2025May 2, 2025

    • ultramicrotome

      Public
      Blender/Python tool for simulating an ultramicrotome for 3DEM analysis
      GNU General Public License v2.0
      •0•0•0•0•Updated Feb 14, 2025Feb 14, 2025

    • article_mcell4_1

      Public
      This repository contains data and models for the MCell4 article
      Python
      •1•0•0•0•Updated Apr 12, 2023Apr 12, 2023

    • cellblender_tutorials

      Public
      CellBlender Tutorials
      cellblendermcell-tutorials
      cellblendermcell-tutorials
      JavaScript
      •1•3•3•4•Updated Dec 26, 2022Dec 26, 2022

    • Workshop_2022

      Public
      GH repository for MMBioS Cell Modeling Workshop happening between July 11 - 15
      Jupyter Notebook
      •1•2•0•0•Updated Jul 15, 2022Jul 15, 2022

    • neuron_launcher

      Public
      Set of tools in Blender to create models for MCell/Neuron hybrid simulations
      blenderswcneuron-simulations
      blenderswcneuron-simulationsmcellcable-model
      C++
      •2•6•0•1•Updated Jan 12, 2022Jan 12, 2022

    • Workshop_2021

      Public
      Jupyter Notebook
      •2•3•0•0•Updated Jul 17, 2021Jul 17, 2021

    • gamer1

      Public
      Geometry-preserving Adaptive MeshER Version 1
      C++
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Jul 2, 2021Jul 2, 2021

    • add_icos_addon

      Public
      A simple addon used as a Blender python scripting tutorial
      Python
      •0•0•0•0•Updated Jun 11, 2021Jun 11, 2021

    • swc_mesher

      Public
      Creates a Blender Object from an SWC formatted file
      blendermeshmcell
      blendermeshmcellcellblenderneuron-launcher
      Python
      •8•9•2•1•Updated Jun 30, 2020Jun 30, 2020

    • Workshop_2020

      Public
      Repository for models, descriptions, and software supporting the 2020 Workshop
      simulationmcellcellblender
      simulationmcellcellblenderbionetgenmcell-tutorialscellblender-modelcellorganizer
      Jupyter Notebook
      •0•1•0•0•Updated Jun 26, 2020Jun 26, 2020

    • libMCellPP

      Public
      C++ Version of MCell
      Python
      •3•0•0•0•Updated Apr 14, 2020Apr 14, 2020

    • CellBlender_Models

      Public
      Repository for CellBlender Models and Examples
      simulationcellblendercellblender-model
      simulationcellblendercellblender-model
      Python
      •1•0•0•0•Updated Feb 14, 2020Feb 14, 2020

    • Workshop_2019

      Public
      Repository for models, descriptions, and software supporting the 2019 Workshop
      Jupyter Notebook
      •4•2•0•0•Updated May 14, 2019May 14, 2019

    • mcell_web

      Public
      Provides a simple web interface for running MCell
      mcell
      mcell
      PHP
      •0•0•0•0•Updated Nov 14, 2018Nov 14, 2018

    • nutmeg

      Public
      nutmeg is a concurrent regression test framework for the MCell simulator
      Go
      •
      BSD 2-Clause "Simplified" License
      •2•1•2•0•Updated Aug 28, 2018Aug 28, 2018

    • mcellRules

      Public
      Rule Based Modeling using MCell, NFsim, and bionetgen
      mcellbionetgen
      mcellbionetgen
      Jupyter Notebook
      •3•0•0•0•Updated Aug 9, 2018Aug 9, 2018

    • gamer-v1

      Public
      Geometry-preserving Adaptive Mesh Generator
      meshblender-addon
      meshblender-addon
      C++
      •
      GNU General Public License v2.0
      •7•7•1•0•Updated Jul 9, 2018Jul 9, 2018
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