Speakers
Description
CompuCell3D is an open-source multiscale modeling environment for multicellular systems that combines biological realism, computational flexibility, and ease of learning. Based on the cellular Potts/Glazier-Graner-Hogeweg formalism, it supports explicit dynamic cell shape, adhesion, motility, growth, elastic solid-like junctions, filopodia, extracellular transport, and coupling to intracellular regulatory and signaling models encoded in SBML, Antimony, CellML, and MaBoSS. CompuCell3D has also evolved into a Python library, enabling interoperability with other Python-accessible modeling tools, and includes a Vivarium wrapper that allows it to serve as a component in the Vivarium ecosystem. Its high-level model specification, interactive tools, and multithreaded execution on multicore CPUs lower barriers to entry while supporting sophisticated multiscale applications.
Over the past two decades, CompuCell3D has been used in a broad range of applications, including embryonic development, morphogenesis, cancer, angiogenesis, immune response, viral infection, regeneration, tissue engineering, and toxicology. I will present the framework’s core ideas and distinctive capabilities, highlight representative applications, and describe current OpenVT efforts to create reference models supporting reproducibility and output comparability across CPM-based platforms such as CompuCell3D, Morpheus, Artistoo, and CHASTE. This work underscores the central role of open sharing, FAIR and CURE principles, and reproducible model exchange in building a robust community ecosystem for multicellular systems biology.
