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    79 repositories

    • scopyon

      Public
      :microscope: Monte Carlo simulation toolkit for bioimaging systems
      pythonsimulationoptics
      pythonsimulationopticsbioimaging-systems
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•7•6•1•Updated Apr 13, 2026Apr 13, 2026

    • ecell4

      Public
      An integrated software environment for multi-algorithm, multi-timescale, multi-spatial-representation simulation of various cellular phenomena
      Python
      •
      GNU General Public License v3.0
      •9•18•30•1•Updated Apr 6, 2026Apr 6, 2026

    • ecell4_base

      Public
      An integrated software environment for multi-algorithm, multi-timescale, multi-spatial-representation simulation of various cellular phenomena
      pythonc-plus-plussimulation
      pythonc-plus-plussimulationsystems-biologyjupyter-notebook
      C++
      •
      GNU General Public License v3.0
      •22•62•31•1•Updated Apr 2, 2026Apr 2, 2026

    • labcode-web-app

      Public
      TypeScript
      •1•0•0•0•Updated Jan 20, 2026Jan 20, 2026

    • labcode-test-environment

      Public
      Python
      •1•0•0•0•Updated Jan 9, 2026Jan 9, 2026

    • labcode-log-server

      Public
      Python
      •1•0•0•1•Updated Jan 9, 2026Jan 9, 2026

    • labcode-sim

      Public
      Python
      •1•0•0•0•Updated Jan 9, 2026Jan 9, 2026

    • greens_functions

      Public
      C++
      •
      GNU General Public License v2.0
      •0•1•3•0•Updated Nov 20, 2025Nov 20, 2025

    • ofplang

      Public
      The object flow programming language
      Python
      •0•0•0•0•Updated Jun 18, 2025Jun 18, 2025

    • transomics2cytoscape

      Public
      Get and integrate the pathways to create a 3D transomics network visualization
      R
      •0•8•0•0•Updated Oct 28, 2024Oct 28, 2024

    • ECell_Dive

      Public
      C#
      •
      MIT License
      •0•3•0•0•Updated Oct 7, 2024Oct 7, 2024

    • ECell_Engine

      Public
      Real-time simulation engine for biological systems
      C++
      •
      MIT License
      •2•3•0•0•Updated Sep 26, 2024Sep 26, 2024

    • kosmogora

      Public
      Jupyter Notebook
      •
      MIT License
      •1•1•4•0•Updated Oct 31, 2023Oct 31, 2023

    • bioimage_workflows

      Public
      Python
      •2•0•2•3•Updated Mar 14, 2023Mar 14, 2023

    • id2id

      Public
      Python
      •
      MIT License
      •0•0•10•0•Updated Jan 23, 2023Jan 23, 2023

    • transomics2cytoscape-py

      Public
      Automation of the transomics 2.5D network visualization
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 26, 2022Dec 26, 2022

    • SigmoID

      Public
      A Xojo/python tool for identification and annotation of transcription factor binding sites in bacterial genomes
      Xojo
      •
      GNU General Public License v3.0
      •4•0•0•0•Updated Sep 29, 2022Sep 29, 2022

    • transomics2cytoscape-input-datasets

      Public
      0•0•0•0•Updated Jun 27, 2022Jun 27, 2022

    • dash-pathway

      Public
      A Dash component for pathway visualization
      Python
      •
      MIT License
      •0•2•9•1•Updated Jun 16, 2022Jun 16, 2022

    • greens_functions11

      Public
      C++
      •0•0•0•0•Updated Jul 11, 2021Jul 11, 2021

    • ecell4_docs

      Public
      The Sphinx source for https://ecell4.e-cell.org/
      pythonsystems-biologyjupyter-notebook
      pythonsystems-biologyjupyter-notebook
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •5•2•13•2•Updated May 8, 2021May 8, 2021

    • kedro-bioimage

      Public
      Python
      •0•0•5•0•Updated Nov 30, 2020Nov 30, 2020

    • manylinux-dockerimage

      Public
      Base Docker image for building ecell4_base manylinux wheel
      Dockerfile
      •0•0•0•0•Updated Sep 18, 2020Sep 18, 2020

    • blog

      Public
      The Hugo source for https://blog.e-cell.org
      HTML
      •0•0•0•0•Updated Jun 4, 2020Jun 4, 2020

    • ecell-website

      Public
      The Sphinx source for https://www.e-cell.org/
      Python
      •0•0•4•0•Updated Jun 3, 2020Jun 3, 2020

    • ecell4_base-feedstock

      Public
      A conda-smithy repository for ecell4_base.
      Shell
      •
      BSD 3-Clause "New" or "Revised" License
      •4•0•0•0•Updated Apr 14, 2020Apr 14, 2020

    • staged-recipes

      Public
      A place to submit conda recipes before they become fully fledged conda-forge feedstocks
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5.9k•0•0•0•Updated Jan 3, 2020Jan 3, 2020

    • dash-bio

      Public
      Open-source bioinformatics components for Dash
      Python
      •
      MIT License
      •191•0•0•0•Updated Dec 31, 2019Dec 31, 2019

    • ecell4_hugo

      Public
      0•0•0•0•Updated Dec 29, 2019Dec 29, 2019

    • ecell_hugo

      Public
      CSS
      •1•0•1•0•Updated Dec 22, 2019Dec 22, 2019
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