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    45 repositories

    • vivarium-collective.github.io

      Public
      HTML
      •0•0•1•0•Updated Feb 7, 2025Feb 7, 2025

    • vivarium-interface

      Public
      Vivarium 2.0 Interface to Process-Bigraphs
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•1•Updated Feb 5, 2025Feb 5, 2025

    • bigraph-schema

      Public
      compositional type schemas
      Python
      •
      Apache License 2.0
      •2•1•36•0•Updated Feb 5, 2025Feb 5, 2025

    • cdFBA

      Public
      Community Dynamic Flux Balance Analysis using process-bigraph
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 4, 2025Feb 4, 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 4, 2025Feb 4, 2025

    • process-bigraph

      Public
      process and composite simulation interfaces
      Jupyter Notebook
      •
      Apache License 2.0
      •2•2•31•0•Updated Jan 31, 2025Jan 31, 2025

    • spatio-flux

      Public
      spatio-temporal fba for process-bigraphs
      Python
      •1•1•1•0•Updated Jan 29, 2025Jan 29, 2025

    • v2Ecoli

      Public
      Whole cell model of E. coli implemented with process-bigraph
      Jupyter Notebook
      •
      MIT License
      •4•0•0•0•Updated Jan 28, 2025Jan 28, 2025

    • multicell-schema

      Public
      Jupyter Notebook
      •1•1•1•0•Updated Jan 27, 2025Jan 27, 2025

    • bigraph-viz

      Public
      visualization tool for bigraph schema
      Jupyter Notebook
      •
      Apache License 2.0
      •1•0•0•1•Updated Jan 18, 2025Jan 18, 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•27•16•0•Updated Dec 3, 2024Dec 3, 2024

    • vivarium-simservice

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 1, 2024Nov 1, 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•2•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

    • vivarium-bioscrape

      Public
      An interface to allow Vivarium to simulate Chemical Reaction Networks (CRNs) using the Bioscrape package and to automatically create ports between CRNs.
      crns
      HTML
      •
      MIT License
      •0•1•0•1•Updated Jun 14, 2023Jun 14, 2023