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viva-tumor-Vivarium-2
A process-bigraph port of the multiscale agent-based tumor microenvironment model, including tumor, T-cell, and dendritic-cell biology, diffusing IFNg and tumor-debris fields, and cell-cell neighbor exchange.
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.
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-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.
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.