From single models to community advances: open source codes and data standards

Paul Macklin (March 27, 2017)

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Abstract

Problems in tissue engineering, developmental biology, cancer, and related areas require that we study 3-D multicellular systems, coupling dynamics at many scales such as protein signaling, cell phenotype "decisions," biotransport, and mechanics. Developing, calibrating, and validating models to study these systems requires not only sophisticated tools, but also a huge variety of data ranging from molecular to clinical scales. No one research team can develop all the necessary software and gather all the required data on their own, so we present our recent work to (1) contribute scalable open source software to simulate 3-D biotransport of many substrates (BioFVM), 3-D multicellular systems (PhysiCell), and extraction of cell phenotype from high-throughput experiments (CellPD), (2) help build a community for collaboration by creating a standard for multicellular data (MultiCellDS), and (3) work with this community to link biosimulation software and open data repositories through data standards.