35 projects
viva-cpm
A process-bigraph Cellular Potts Model framework: a fast Rust CPM engine (2D/3D) with pluggable subcellular models, structural constraints, and metrics.
viva-munk
multi-cell simulations with pymunk 2d physics
viva-tumor-tcell
Process-bigraph port of the tumor-tcell tumor-microenvironment ABM (viva-munk physics)
viva-tellurium
Process-bigraph wrapper for Tellurium / libroadrunner SBML simulation
viva-emitters
Focused emitter library for process-bigraph composites — SQLite, Parquet, and beyond
process-bigraph
protocol and execution for compositional systems biology
vivarium-workbench
Web-based workbench for Vivarium / process-bigraph workspaces
viva-catalog
Ecosystem ledger for the vivarium / process-bigraph workbench: the registry of repos + an aggregated artifact index.
viva-superpowers
Plugin Python helpers for the viva-superpowers skills (was pbg-superpowers)
pbg-superpowers
Deprecated alias — the package was renamed to 'viva-superpowers'. This shim just depends on it so existing 'pbg-superpowers' PyPI deps keep resolving. Import 'viva_superpowers' (a 'pbg_superpowers' import shim also ships in viva-superpowers).
bigraph-schema
A serializable type schema for compositional systems biology
viva-workspace
Shared source of truth for viva workspace-layout logic (layout map, root-walker, study resolver, canonical outcomes, package naming).
pbg-emitters
Focused emitter library for process-bigraph composites — SQLite, Parquet, and beyond
pbg-basic-processes
Reusable, composite-agnostic process-bigraph processes — Clock, Intervention, MathExpression, and beyond
investigation-contracts
Shared bigraph-schema types for the Actionable Investigation Graph (RFC-0002).
bigraph-viz2
Lightweight read-only bigraph renderer with no graphviz dependency
bigraph-viz
A visualization method for displaying the structure of process bigraphs
multi-cell
multi-cell simulations with pymunk 2d physics
vivarium-interface
None
vivarium-core
Engine for composing and simulating computational biology models with the Vivarium interface.
vivarium-simservice
None
tumor-tcell
bigraph-builder
sed2
vivarium-convenience
provides a vivarium process with a configurable convenience kinetics
vivarium-multibody
vivarium-cell
A collection of models for simulating cells with Vivarium.
vivarium-notebooks
vivarium-cobra
vivarium-smoldyn
vivarium-bioscrape
vivarium-scripts
miscellaneous scripts for vivarium projects
