Vivarium Collective

home of the vivarium core engine and project ecosystem

Pinned Repositories

array_of_oscillating_cells
Language:Component Pascal1 2 00
bigraph-schema
compositional type schemas
Language:Python1 2 812
bigraph-viz
visualization tool for bigraph schema
Language:Jupyter Notebook0 2 01
process-bigraph
Language:Jupyter Notebook2 2 622
tumor-tcell
Language:Jupyter Notebook2 3 00
vivarium-bioscrape
An interface to allow Vivarium to simulate Chemical Reaction Networks (CRNs) using the Bioscrape package and to automatically create ports between CRNs.
Language:HTML1 10 00
vivarium-cell
A collection of models for simulating cells with Vivarium.
Language:Python5 4 02
vivarium-core
Core Interface and Engine for Vivarium
Language:Python26 5 433
vivarium-notebooks
Language:Jupyter Notebook5 5 30
vivarium-template
A template for building models with Vivarium.
Language:Python3 5 00

Vivarium Collective's Repositories

vivarium-collective/vivarium-core
Core Interface and Engine for Vivarium
Language:Python26 5 433
vivarium-collective/vivarium-template
A template for building models with Vivarium.
Language:Python3 5 00
vivarium-collective/process-bigraph
Language:Jupyter Notebook2 2 622
vivarium-collective/tumor-tcell
Language:Jupyter Notebook2 3 00
vivarium-collective/array_of_oscillating_cells
Language:Component Pascal1 2 00
vivarium-collective/bigraph-schema
compositional type schemas
Language:Python1 2 812
vivarium-collective/biosimulator-processes
Core implementations of simulator processes using the process-bigraph Process API
Language:Jupyter Notebook11
vivarium-collective/multicell-schema
Language:Python1
vivarium-collective/spatio-flux
spatio-temporal fba for process-bigraphs
Language:Python11
vivarium-collective/vivarium-bioscrape
An interface to allow Vivarium to simulate Chemical Reaction Networks (CRNs) using the Bioscrape package and to automatically create ports between CRNs.
Language:HTML1 10 00
vivarium-collective/vivarium-biosimulators
A Vivarium wrapper for BioSimulators
Language:Jupyter Notebook1 3 80
vivarium-collective/vivarium-tellurium
Language:Python10
vivarium-collective/bigraph-viz
visualization tool for bigraph schema
Language:Jupyter Notebook0 2 01
vivarium-collective/Microbiome
Language:Jupyter Notebook0 2 00
vivarium-collective/vivarium-collective.github.io
Language:HTML0 4 10
vivarium-collective/bigraph-builder
Language:Jupyter Notebook2 0
vivarium-collective/bio-assist
OpenAI and LLM browser based biological modeling and simulation assistant.
Language:Jupyter Notebook
vivarium-collective/bio-bundles
Commonly grouped biological composites
Language:Jupyter Notebook
vivarium-collective/biosimulator-processes-api
REST API which interacts with the biosimulator-processes tooling.
Language:Python
vivarium-collective/cdFBA
Community Dynamic Flux Balance Analysis using process-bigraph
Language:Python
vivarium-collective/compucell-tissueforge
Process-Bigraph composition of CompuCell3D and TissueForge
Language:Python1
vivarium-collective/diatom
Language:Jupyter Notebook
vivarium-collective/hypoxia-oscillations
Language:Jupyter Notebook1
vivarium-collective/mongo-emitter
process-bigraph emitter with MongoDB
Language:Python2 0
vivarium-collective/smoldyn-process
A Smoldyn based wrapper of Process Bigraphs
Language:Python
vivarium-collective/vivarium-bayesian-mca
Language:Jupyter Notebook
vivarium-collective/vivarium-cellpack
a process for composing cellpack into vivarium simulations
Language:Python2 0
vivarium-collective/vivarium-MICOM
Language:Jupyter Notebook
vivarium-collective/vivarium-ReaDDy
Language:Python3 0
vivarium-collective/vivarium-simservice
Language:Python2 0