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    58 repositories

    • vivarium-collective.github.io

      Public
      HTML
      •0•0•1•0•Updated Aug 21, 2025Aug 21, 2025

    • sms-api

      Public
      SMS API
      Python
      •
      Other
      •0•0•0•2•Updated Aug 20, 2025Aug 20, 2025

    • vivarium-tyssue

      Public
      Vivarium Implementation of a Tyssue Crypt Model
      Jupyter Notebook
      •0•0•0•0•Updated Aug 20, 2025Aug 20, 2025

    • bigraph-schema

      Public
      compositional type schemas
      Python
      •
      Apache License 2.0
      •3•1•43•2•Updated Aug 19, 2025Aug 19, 2025

    • julia-process

      Public
      containerized julia program that acts as a vivarium process
      Julia
      •0•0•0•0•Updated Aug 15, 2025Aug 15, 2025

    • vEcoli

      Public
      Whole cell model of E. coli implemented with process-bigraph (in development)
      Jupyter Notebook
      •
      MIT License
      •12•1•0•2•Updated Aug 14, 2025Aug 14, 2025

    • process-bigraph

      Public
      process and composite simulation interfaces
      Python
      •
      Apache License 2.0
      •3•2•32•0•Updated Aug 13, 2025Aug 13, 2025

    • vivatyssue

      Public
      An epithelium simulation library
      Python
      •
      GNU General Public License v3.0
      •23•0•0•0•Updated Aug 7, 2025Aug 7, 2025

    • spatio-flux

      Public
      spatio-temporal fba for process-bigraphs
      Python
      •1•1•1•0•Updated Aug 7, 2025Aug 7, 2025

    • cdFBA

      Public
      Community Dynamic Flux Balance Analysis using process-bigraph
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 5, 2025Aug 5, 2025

    • simdata-visualization

      Public
      A visualization of the simdata object for vivarium Ecoli
      Python
      •0•0•0•0•Updated Aug 4, 2025Aug 4, 2025

    • bigraph-viz

      Public
      visualization tool for bigraph schema
      Jupyter Notebook
      •
      Apache License 2.0
      •1•1•0•0•Updated Jul 30, 2025Jul 30, 2025

    • vivarium-interface

      Public
      Vivarium 2.0 Interface to Process-Bigraphs
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•2•2•Updated Jul 26, 2025Jul 26, 2025

    • process-template

      Public template
      A starting point for vivarium projects
      Python
      •0•0•0•0•Updated Jul 26, 2025Jul 26, 2025

    • genEcoli

      Public
      Generative Whole-cell E. Coli model
      0•0•0•2•Updated Jul 11, 2025Jul 11, 2025

    • CRM

      Public
      Consumer Resource Models
      Jupyter Notebook
      •0•0•0•0•Updated Jul 10, 2025Jul 10, 2025

    • spatial-transport

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jun 23, 2025Jun 23, 2025

    • greymatter

      Public
      A pedagogical exploration of hypergraphs and their dynamics
      Python
      •0•0•0•0•Updated Jun 10, 2025Jun 10, 2025

    • benchmark-storage

      Public
      Benchmark Xarray/Zarr and DuckDB/Parquet storage format ffor whole-cell modeling output data
      Python
      •1•0•0•0•Updated May 31, 2025May 31, 2025

    • vivarium-kecoli

      Public
      Towards vivarium implementation of E. coli kinetic metabolic models
      Jupyter Notebook
      •0•0•0•0•Updated May 12, 2025May 12, 2025

    • multicell-schema

      Public
      Jupyter Notebook
      •1•1•1•0•Updated Apr 18, 2025Apr 18, 2025

    • vivarium-demos

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Apr 16, 2025Apr 16, 2025

    • biosimulator-processes

      Public
      Core implementations of simulator processes using the process-bigraph Process API
      Jupyter Notebook
      •
      Apache License 2.0
      •1•1•0•0•Updated Apr 7, 2025Apr 7, 2025

    • vivarium-multibody

      Public
      Vivarium processes for 2D multi-cell physics
      Jupyter Notebook
      •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

    • vivarium-simservice

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 7, 2025Feb 7, 2025

    • RashmiRotationProject---Microbial-Metabolic-Modeling-and-Analysis

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Dec 5, 2024Dec 5, 2024

    • vivarium-core

      Public
      Core Interface and Engine for Vivarium 1.0
      enginemulti-scalevivarium
      Python
      •
      Apache License 2.0
      •3•33•16•0•Updated Dec 3, 2024Dec 3, 2024

    • compucell-tissueforge

      Public
      Process-Bigraph composition of CompuCell3D and TissueForge
      Python
      •1•0•0•0•Updated Nov 1, 2024Nov 1, 2024

    • bio-bundles

      Public
      Commonly grouped biological composites
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 16, 2024Oct 16, 2024

    • vivarium-MICOM

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Sep 10, 2024Sep 10, 2024