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@vivarium-collective

Vivarium Collective

home of the vivarium project ecosystem

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  1. vivarium-core vivarium-core Public

    Core Interface and Engine for Vivarium 1.0

    Python 35 3

  2. process-bigraph process-bigraph Public

    Vivarium 2.0 simulation interfaces

    Jupyter Notebook 5 4

  3. bigraph-schema bigraph-schema Public

    compositional type schemas

    Python 2 4

  4. bigraph-viz bigraph-viz Public

    visualization tool for bigraph schema

    Jupyter Notebook 1 2

  5. process-template process-template Public template

    A starting point for vivarium projects

    Python

  6. spatio-flux spatio-flux Public

    spatio-temporal microbial simulations with Vivarium 2.0

    Python 1 2

Repositories

Showing 10 of 71 repositories
  • vivarium-collective/vivarium-collective.github.io’s past year of commit activity
    HTML 0 0 1 0 Updated Feb 13, 2026
  • vEcoli Public Forked from CovertLab/vEcoli

    Whole cell model of E. coli implemented with process-bigraph (in development)

    vivarium-collective/vEcoli’s past year of commit activity
    Jupyter Notebook 1 MIT 15 0 4 Updated Feb 12, 2026
  • vEcolisRNA Public

    Modeling sigma-factor based gene transcription in E. coli

    vivarium-collective/vEcolisRNA’s past year of commit activity
    Jupyter Notebook 0 MIT 1 0 1 Updated Feb 12, 2026
  • vivarium-collective/vEcoli-spatial-voronoi’s past year of commit activity
    Python 0 MIT 0 0 1 Updated Feb 12, 2026
  • sms-api Public

    SMS API - Design, run, and analyze simulations of dynamic cellular processes in Escherichia coli.

    vivarium-collective/sms-api’s past year of commit activity
    Python 3 0 3 8 Updated Feb 11, 2026
  • bigraph-schema Public

    compositional type schemas

    vivarium-collective/bigraph-schema’s past year of commit activity
    Python 2 Apache-2.0 4 35 1 Updated Feb 3, 2026
  • biocompose Public
    vivarium-collective/biocompose’s past year of commit activity
    Python 0 0 0 0 Updated Jan 30, 2026
  • vivarium-tyssue Public

    Vivarium Implementation of a Tyssue Euler Methods

    vivarium-collective/vivarium-tyssue’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Jan 28, 2026
  • vivatyssue Public Forked from DamCB/tyssue

    An epithelium simulation library

    vivarium-collective/vivatyssue’s past year of commit activity
    Python 2 GPL-3.0 22 0 1 Updated Jan 28, 2026
  • process-bigraph Public

    Vivarium 2.0 simulation interfaces

    vivarium-collective/process-bigraph’s past year of commit activity
    Jupyter Notebook 5 Apache-2.0 4 31 0 Updated Jan 13, 2026

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