Samuel H. Friedman

This paper introduces a high-throughput framework integrating PhysiCell and EMEWS to test cancer hypotheses through mechanistic simulations and optimize therapeutic strategies.

Open source off-lattice agent-based C++ simulator PhysiCell, coupled to the BioFVM diffusion solver, simulates 3-D multicellular tissues with cost linear in cell number, reaching roughly 10^6 cells.

The paper reviews open source software and data standards in multicellular systems biology and highlights areas for growth to enable community-driven frameworks.

This paper develops a mathematical model to account for biological and technical variability in cell proliferation assays and shows how these factors affect growth rate measurements.

The paper introduces MultiCellDS, a standard and community-driven initiative for sharing multicellular data to enhance research in cell biology.

The paper introduces MultiCellDS, a standard for multicellular data curation, and presents MultiCellDB as a database to store associated data, enhancing data sharing and utility in biological and clinical research.

The paper describes a method to estimate cell cycle model parameters using optimization tools with flow cytometry and synthetic viability data, demonstrated on simulated data.

The paper introduces PhysiCell, an agent-based model for simulating tumor growth in 3-D microenvironments, and reports its scalability to large cell systems.

The paper introduces BioFVM, a reaction-diffusion solver for simulating chemical transport in 3-D tissues, supporting multiple compounds and demonstrating efficient computational scaling.