Repositories list

• 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

  •99 forks in ecell/ecell4•2020 stars in ecell/ecell4•3030 issues in ecell/ecell4•11 pull request in ecell/ecell4•Updated Sep 23, 2026Sep 23, 2026

• scopyon

  Public

  ecell/scopyon’s past year of commit activity
  :microscope: Monte Carlo simulation toolkit for bioimaging systems

  pythonsimulationoptics+ 1

  pythonsimulationopticsbioimaging-systems

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •44 forks in ecell/scopyon•77 stars in ecell/scopyon•66 issues in ecell/scopyon•11 pull request in ecell/scopyon•Updated Sep 21, 2026Sep 21, 2026

• ecell4_base

  Public

  ecell/ecell4_base’s past year of commit activity
  An integrated software environment for multi-algorithm, multi-timescale, multi-spatial-representation simulation of various cellular phenomena

  pythonc-plus-plussimulation+ 2

  pythonc-plus-plussimulationsystems-biologyjupyter-notebook

  C++

  •

  GNU General Public License v3.0

  •2222 forks in ecell/ecell4_base•6363 stars in ecell/ecell4_base•3131 issues in ecell/ecell4_base•11 pull request in ecell/ecell4_base•Updated Jun 24, 2026Jun 24, 2026

• labcode-web-app

  Public
  TypeScript

  •11 fork in ecell/labcode-web-app•00 stars in ecell/labcode-web-app•00 issues in ecell/labcode-web-app•00 pull requests in ecell/labcode-web-app•Updated Jan 20, 2026Jan 20, 2026

• labcode-test-environment

  Public
  Python

  •11 fork in ecell/labcode-test-environment•00 stars in ecell/labcode-test-environment•00 issues in ecell/labcode-test-environment•00 pull requests in ecell/labcode-test-environment•Updated Jan 9, 2026Jan 9, 2026

• labcode-log-server

  Public

  ecell/labcode-log-server’s past year of commit activity
  Python

  •11 fork in ecell/labcode-log-server•00 stars in ecell/labcode-log-server•00 issues in ecell/labcode-log-server•11 pull request in ecell/labcode-log-server•Updated Jan 9, 2026Jan 9, 2026

• labcode-sim

  Public

  ecell/labcode-sim’s past year of commit activity
  Python

  •11 fork in ecell/labcode-sim•00 stars in ecell/labcode-sim•00 issues in ecell/labcode-sim•00 pull requests in ecell/labcode-sim•Updated Jan 9, 2026Jan 9, 2026

• greens_functions

  Public

  ecell/greens_functions’s past year of commit activity
  C++

  •

  GNU General Public License v2.0

  •00 forks in ecell/greens_functions•11 star in ecell/greens_functions•33 issues in ecell/greens_functions•00 pull requests in ecell/greens_functions•Updated Nov 20, 2025Nov 20, 2025

• ofplang

  Public

  ecell/ofplang’s past year of commit activity
  The object flow programming language

  Python

  •00 forks in ecell/ofplang•00 stars in ecell/ofplang•00 issues in ecell/ofplang•00 pull requests in ecell/ofplang•Updated Jun 18, 2025Jun 18, 2025

• transomics2cytoscape

  Public

  ecell/transomics2cytoscape’s past year of commit activity
  Get and integrate the pathways to create a 3D transomics network visualization

  R

  •00 forks in ecell/transomics2cytoscape•88 stars in ecell/transomics2cytoscape•00 issues in ecell/transomics2cytoscape•00 pull requests in ecell/transomics2cytoscape•Updated Oct 28, 2024Oct 28, 2024

• ECell_Dive

  Public
  C#

  •

  MIT License

  •00 forks in ecell/ECell_Dive•33 stars in ecell/ECell_Dive•00 issues in ecell/ECell_Dive•00 pull requests in ecell/ECell_Dive•Updated Oct 7, 2024Oct 7, 2024

• ECell_Engine

  Public
  Real-time simulation engine for biological systems

  C++

  •

  MIT License

  •22 forks in ecell/ECell_Engine•33 stars in ecell/ECell_Engine•00 issues in ecell/ECell_Engine•00 pull requests in ecell/ECell_Engine•Updated Sep 26, 2024Sep 26, 2024

• kosmogora

  Public
  Jupyter Notebook

  •

  MIT License

  •11 fork in ecell/kosmogora•11 star in ecell/kosmogora•44 issues in ecell/kosmogora•00 pull requests in ecell/kosmogora•Updated Oct 31, 2023Oct 31, 2023

• bioimage_workflows

  Public
  Python

  •22 forks in ecell/bioimage_workflows•00 stars in ecell/bioimage_workflows•22 issues in ecell/bioimage_workflows•33 pull requests in ecell/bioimage_workflows•Updated Mar 14, 2023Mar 14, 2023

• id2id

  Public
  Python

  •

  MIT License

  •00 forks in ecell/id2id•00 stars in ecell/id2id•1010 issues in ecell/id2id•00 pull requests in ecell/id2id•Updated Jan 23, 2023Jan 23, 2023

• transomics2cytoscape-py

  Public
  Automation of the transomics 2.5D network visualization

  Python

  •

  MIT License

  •00 forks in ecell/transomics2cytoscape-py•00 stars in ecell/transomics2cytoscape-py•00 issues in ecell/transomics2cytoscape-py•00 pull requests in ecell/transomics2cytoscape-py•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

  •44 forks in ecell/SigmoID•00 stars in ecell/SigmoID•00 issues in ecell/SigmoID•00 pull requests in ecell/SigmoID•Updated Sep 29, 2022Sep 29, 2022

• transomics2cytoscape-input-datasets

  Public
  00 forks in ecell/transomics2cytoscape-input-datasets•00 stars in ecell/transomics2cytoscape-input-datasets•00 issues in ecell/transomics2cytoscape-input-datasets•00 pull requests in ecell/transomics2cytoscape-input-datasets•Updated Jun 27, 2022Jun 27, 2022

• dash-pathway

  Public
  A Dash component for pathway visualization

  Python

  •

  MIT License

  •00 forks in ecell/dash-pathway•22 stars in ecell/dash-pathway•99 issues in ecell/dash-pathway•11 pull request in ecell/dash-pathway•Updated Jun 16, 2022Jun 16, 2022

• greens_functions11

  Public
  C++

  •00 forks in ecell/greens_functions11•00 stars in ecell/greens_functions11•00 issues in ecell/greens_functions11•00 pull requests in ecell/greens_functions11•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

  •55 forks in ecell/ecell4_docs•22 stars in ecell/ecell4_docs•1313 issues in ecell/ecell4_docs•22 pull requests in ecell/ecell4_docs•Updated May 8, 2021May 8, 2021

• kedro-bioimage

  Public
  Python

  •00 forks in ecell/kedro-bioimage•00 stars in ecell/kedro-bioimage•55 issues in ecell/kedro-bioimage•00 pull requests in ecell/kedro-bioimage•Updated Nov 30, 2020Nov 30, 2020

• manylinux-dockerimage

  Public
  Base Docker image for building ecell4_base manylinux wheel

  Dockerfile

  •00 forks in ecell/manylinux-dockerimage•00 stars in ecell/manylinux-dockerimage•00 issues in ecell/manylinux-dockerimage•00 pull requests in ecell/manylinux-dockerimage•Updated Sep 18, 2020Sep 18, 2020

• blog

  Public
  The Hugo source for https://blog.e-cell.org

  HTML

  •00 forks in ecell/blog•00 stars in ecell/blog•00 issues in ecell/blog•00 pull requests in ecell/blog•Updated Jun 4, 2020Jun 4, 2020

• ecell-website

  Public
  The Sphinx source for https://www.e-cell.org/

  Python

  •00 forks in ecell/ecell-website•00 stars in ecell/ecell-website•44 issues in ecell/ecell-website•00 pull requests in ecell/ecell-website•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

  •44 forks in ecell/ecell4_base-feedstock•00 stars in ecell/ecell4_base-feedstock•00 issues in ecell/ecell4_base-feedstock•00 pull requests in ecell/ecell4_base-feedstock•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

  •6.5k6.5k forks in ecell/staged-recipes•00 stars in ecell/staged-recipes•00 issues in ecell/staged-recipes•00 pull requests in ecell/staged-recipes•Updated Jan 3, 2020Jan 3, 2020

• dash-bio

  Public
  Open-source bioinformatics components for Dash

  Python

  •

  MIT License

  •191191 forks in ecell/dash-bio•00 stars in ecell/dash-bio•00 issues in ecell/dash-bio•00 pull requests in ecell/dash-bio•Updated Dec 31, 2019Dec 31, 2019

• ecell4_hugo

  Public
  00 forks in ecell/ecell4_hugo•00 stars in ecell/ecell4_hugo•00 issues in ecell/ecell4_hugo•00 pull requests in ecell/ecell4_hugo•Updated Dec 29, 2019Dec 29, 2019

• ecell_hugo

  Public
  CSS

  •11 fork in ecell/ecell_hugo•00 stars in ecell/ecell_hugo•11 issue in ecell/ecell_hugo•00 pull requests in ecell/ecell_hugo•Updated Dec 22, 2019Dec 22, 2019