Open source discrete and agent-based modeling frameworks for biology

This is an actively curated collection of open source frameworks for building multicellular simulations in biology.

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This is an actively curated collection of open source frameworks for building multicellular simulations in biology. If you spot a software framework that should be included here, please contact Paul Macklin. See http://MathCancer.org/Contact.php.

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 Main image credit: A discrete simulation of immune cells (red) attacking a tumor with heterogeneous immunogenicity (shaded from blue to yellow). Simulated in PhysiCell by Ghaffarizadeh et al [1]. [1] http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005991 Background image credit: A discrete simulation of cancer metastases growing in liver tissue. Simulated in PhysiCell [1][1] http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005991 Keywords: agent-based model, simulation, computational biology, discrete model, individual-based model DOI: 10.14293/S2199-1006.1.SOR-UNCAT.CLYWCCG.v1