Repositories list

• vivarium-collective.github.io

  Public
  HTML

  •0•0•1•0•Updated Mar 9, 2025Mar 9, 2025

• cdFBA

  Public
  Community Dynamic Flux Balance Analysis using process-bigraph

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Mar 4, 2025Mar 4, 2025

• vivarium-interface

  Public
  Vivarium 2.0 Interface to Process-Bigraphs

  Jupyter Notebook

  •

  Apache License 2.0

  •0•0•1•0•Updated Mar 1, 2025Mar 1, 2025

• process-bigraph

  Public
  process and composite simulation interfaces

  Jupyter Notebook

  •

  Apache License 2.0

  •2•2•28•1•Updated Mar 1, 2025Mar 1, 2025

• multicell-schema

  Public
  Jupyter Notebook

  •1•1•1•0•Updated Feb 28, 2025Feb 28, 2025

• bigraph-schema

  Public
  compositional type schemas

  Python

  •

  Apache License 2.0

  •2•1•35•0•Updated Feb 28, 2025Feb 28, 2025

• bigraph-viz

  Public
  visualization tool for bigraph schema

  Jupyter Notebook

  •

  Apache License 2.0

  •1•0•0•0•Updated Feb 22, 2025Feb 22, 2025

• spatio-flux

  Public
  spatio-temporal fba for process-bigraphs

  Python

  •1•1•1•0•Updated Feb 21, 2025Feb 21, 2025

• vivarium-multibody

  Public
  Vivarium processes for 2D multi-cell physics

  Jupyter Notebook

  •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

• biosimulator-processes

  Public
  Core implementations of simulator processes using the process-bigraph Process API

  Jupyter Notebook

  •

  Apache License 2.0

  •1•1•0•1•Updated Feb 19, 2025Feb 19, 2025

• vivarium-simservice

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 7, 2025Feb 7, 2025

• v2Ecoli

  Public
  Whole cell model of E. coli implemented with process-bigraph

  Jupyter Notebook

  •

  MIT License

  •5•0•0•0•Updated Jan 28, 2025Jan 28, 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•28•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

• diatom

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Aug 12, 2024Aug 12, 2024

• array_of_oscillating_cells

  Public
  Component Pascal

  •0•1•0•0•Updated Aug 6, 2024Aug 6, 2024

• hypoxia-oscillations

  Public
  Jupyter Notebook

  •1•0•0•1•Updated Jun 18, 2024Jun 18, 2024

• bio-assist

  Public
  OpenAI and LLM browser based biological modeling and simulation assistant.

  Jupyter Notebook

  •

  Apache License 2.0

  •0•0•0•0•Updated Jun 11, 2024Jun 11, 2024

• biosimulator-processes-api

  Public
  REST API which interacts with the biosimulator-processes tooling.

  Python

  •0•0•0•0•Updated May 17, 2024May 17, 2024

• tumor-tcell

  Public
  Jupyter Notebook

  •0•3•0•0•Updated Mar 4, 2024Mar 4, 2024

• mongo-emitter

  Public
  process-bigraph emitter with MongoDB

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Feb 27, 2024Feb 27, 2024

• vivarium-bayesian-mca

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jan 19, 2024Jan 19, 2024

• smoldyn-process

  Public
  A Smoldyn based wrapper of Process Bigraphs

  Python

  •0•0•0•0•Updated Dec 18, 2023Dec 18, 2023

• Microbiome

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •0•0•0•1•Updated Dec 15, 2023Dec 15, 2023

• vivarium-tellurium

  Public
  Python

  •0•1•0•0•Updated Sep 6, 2023Sep 6, 2023

• vivarium-template

  Public template
  A template for building models with Vivarium.

  Python

  •0•3•0•0•Updated Jul 25, 2023Jul 25, 2023

• vivarium-biosimulators

  Public
  A Vivarium wrapper for BioSimulators

  Jupyter Notebook

  •0•1•5•0•Updated Jul 24, 2023Jul 24, 2023