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Covasim
Covasim performs projections of indicators such as numbers of infections and peak hospital demand, and explores interventions including social distancing, school closures, testing, contact tracing, quarantine, and vaccination.
viva-amici
A process-bigraph bridge that compiles Antimony or SBML models into AMICI per-model C++/SWIG extensions and integrates them with SUNDIALS CVODES, exposing time-stepped and one-shot simulation processes plus exponential-decay, Lotka-Volterra, and MAPK cascade composites.
viva-simbio
A process-bigraph wrapper for simbio that represents chemical reaction networks using Antimony or reaction specifications, rebuilds Antimony through libantimony and libSBML, and integrates the resulting ODEs with simbio's LSODA solver. Species concentrations are exposed through shared stores and emitted as additive per-step deltas.
viva-munk
A composable framework for simulating populations of growing, dividing cells with realistic 2D physics and shared chemical environments. Cells are capsule-shaped rigid bodies or multi-segment compound bodies that grow, divide, secrete particles, attach to surfaces, and interact physically through collisions and confinement; concentration fields use finite-difference diffusion and are coupled to cells through exchange steps.
Spatio-Flux
Spatio-Flux composes independently developed processes including metabolism, spatial transport, particle dynamics, and structural rewrites into executable simulations through typed interfaces and shared orchestration.
mbmm
A general implementation of the Mechanistic Bayesian Mixture Model framework that embeds an application-specific ordinary differential equation trajectory model inside a Bayesian mixture likelihood evaluated against Approximate Bayesian Computation reference banks, with covariate-linked logistic or multinomial gates.
Vivarium-chemotaxis
A Vivarium model integrating receptor activity, flagellar motility, gene expression, transport, metabolism, membrane potential, growth, and division for Escherichia coli chemotaxis.
Vivarium-chemotaxis
The repository implements Vivarium processes and composites for Escherichia coli chemotaxis, including chemoreceptor activity, flagella activity, proton motive force, and integrated metabolism, transport, transcription, translation, complexation, degradation, and division processes.