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Vivarium Users Guide

Module catalog

vivarium-collective/viva-docs

Module catalog¶

Every module here is a ready-to-install unit of capability — a simulator wrapped as process-bigraph Processes, a composite, or a whole workspace — from the Vivarium Collective. Install one into a workspace with /viva-catalog (install <name>), or browse the source on GitHub.

Filter the catalog

Type to search, or click capability tags to narrow the list. There are 27 modules across 22 capability tags.

spatio-flux

spatio-temporal microbial simulations with Vivarium 2.0

microbialmetabolism

/viva-catalog install spatio-flux

v2ecoli

Whole-cell E. coli model in Vivarium 2

whole-cellecoli

/viva-catalog install v2ecoli

viva-amici

Process-bigraph wrapper for AMICI (CVODES-based ODE/DAE simulator). Real bridge to https://github.com/AMICI-dev/AMICI.

ode

/viva-catalog install pbg-amici

viva-biomodels

Process-bigraph workspace: BIOMODELS regression — installs pbg-biomodels-bundle and drives investigations against the BioModels corpus

/viva-catalog install pbg-biomodels

viva-biomodels-bundle

Regression harness for BioModels: runs each model under multiple simulators (COPASI, Tellurium) and renders an interactive comparison report.

/viva-catalog install pbg-biomodels-bundle

viva-bioreactordesign

Process-bigraph wrapper for BioReactorDesign (BiRD) bioreactor simulation

bioreactor

/viva-catalog install pbg-bioreactordesign

viva-caspule

Process-bigraph wrapper for CASPULE (a LAMMPS variant with dynamic bond formation/breaking)

lammps

/viva-catalog install pbg-caspule

viva-comets

Process-bigraph wrapper for COMETS (dynamic FBA + 2D spatial microbial ecosystems)

microbialspatialfba

/viva-catalog install pbg-comets

viva-composite-nfsim-caspule

Process-bigraph composite: CASPULE bond-aware MD coupled to NFSim rule-based kinetics through a configurable observable detector that converts spatial bond clusters into non-spatial species counts.

spatialrule-basedkineticsmdcomposite

/viva-catalog install pbg-composite-nfsim-caspule

viva-compucell3d

Process-bigraph wrapper for the CompuCell3D multicellular simulation environment

multicellular

/viva-catalog install pbg-compucell3d

viva-copasi

process-bigraph-compatible COPASI Steps and Processes for SBML simulation

sbml

/viva-catalog install pbg-copasi

viva-emitters

Focused emitter library for process-bigraph composites

/viva-catalog install viva-emitters

viva-idynomics2

Process-bigraph wrapper for IDynoMiCS 2.0, the Kreft lab's Java-based individual-based biofilm simulator

/viva-catalog install pbg-idynomics2

viva-lammps

Process-bigraph wrapper for the LAMMPS molecular dynamics simulator

lammpsmd

/viva-catalog install pbg-lammps

viva-martini

Process-bigraph wrapper for the Martini coarse-grained force field — membrane systems, micelles, protein-lipid complexes, and vesicles

membranecoarse-grained

/viva-catalog install pbg-martini

viva-medyan

Process-bigraph wrapper for the MEDYAN cytoskeleton simulator: pure-Python re-implementation + a subprocess-driven bridge to the real MEDYAN C++ binary (with checkpoint-restart and HDF5 vesicle support).

cytoskeletonmembrane

/viva-catalog install pbg-medyan

viva-mem3dg

Process-bigraph wrapper for Mem3DG membrane mechanics simulator

membrane

/viva-catalog install pbg-mem3dg

viva-membrane-actin-composite

Process-bigraph composite: pbg-mem3dg + pbg-readdy as a Brownian ratchet (actin pushing on membrane, closed-loop)

membranecompositeparticle

/viva-catalog install pbg-membrane-actin-composite

viva-munk

No description yet.

/viva-catalog install Viva-munk

viva-nfsim

A process-bigraph wrapper for BioNetGen/NFSim

rule-based

/viva-catalog install pbg-nfsim

viva-oxidizeme

Process-bigraph wrapper for OxidizeME — a genome-scale ME-model of E. coli with ROS damage/repair (Yang et al. 2019 PNAS / Palsson lab)

/viva-catalog install pbg-oxidizeme

viva-reactive-system

Process-bigraph wrapper for Milner-style Bigraphical Reactive Systems, with a worked MAPK signalling example.

/viva-catalog install pbg-reactive-system

viva-readdy

Process-bigraph wrapper for the ReaDDy particle-based reaction-diffusion simulator

particlereaction-diffusion

/viva-catalog install pbg-readdy

viva-simbio

Process-bigraph wrapper for simbio (Chemical Reaction Network simulation) — load models from Antimony, simulate with simbio

sbml

/viva-catalog install pbg-simbio

viva-smoldyn

Process-bigraph wrapper for the Smoldyn particle-based spatial stochastic simulator

spatialparticlestochastic

/viva-catalog install pbg-smoldyn

viva-tellurium

Process-bigraph wrapper for Tellurium / libroadrunner SBML & Antimony simulation

sbml

/viva-catalog install pbg-tellurium

viva-vcell-fvsolver

process-bigraph wrapper around pyvcell / pyvcell-fvsolver — VCell's finite-volume 3D reaction-diffusion PDE solver as a PBG Process

reaction-diffusionpde

/viva-catalog install pbg-vcell-fvsolver