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viva-tumor-tcell
A multiscale agent-based tumor microenvironment model with tumor, T-cell, and dendritic-cell processes, diffusing IFNg and tumor-debris fields, cell-cell neighbor exchange, and phenotype conversion/exhaustion dynamics.
Goldbeter1991 - Min Mit Oscil
A minimal model for the mitotic oscillator in early amphibian embryos, representing cyclin-driven activation of cdc2 kinase, cdc2-driven activation of cyclin protease, and delayed negative feedback through cyclin degradation.
Tumor/T cell Microenvironment ABM
The model represents tumor cells, T cells, and related processes in a spatial microenvironment, including intracellular and intercellular interactions, soluble factors, cell movement, molecular fields, proliferation, phenotype changes, and cytotoxic killing. It is implemented on the Vivarium framework and can be initialized with multiplexed imaging datasets.
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.
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.
viva-tumor-tcell
A multiscale agent-based model of the tumor microenvironment with tumor cells, T cells, dendritic cells, diffusing IFNg and tumor-debris fields, and cell-cell neighbor exchange.
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.