PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems
Publication Date
February 23, 2018
Authors
Ahmadreza Ghaffarizadeh, Randy Heiland, Samuel H. Friedman, Shannon M. Mumenthaler, et al
Volume
14
Issue
2
Pages
e1005991
DOI
https://dx.plos.org/10.1371/journal.pcbi.1005991
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1005991
Scopus
85042731473
Mendeley
http://www.mendeley.com/research/physicell-open-source-physicsbased-cell-simulator-3d-multicellular-systems
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Mendeley | Further Information

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Tissue-scale dynamics emerge from systems of many interacting cells as they respond to and influence their microenvironment. The ideal “virtual laboratory” for such multicellular systems simulates both the biochemical microenvironment (the “stage”) and many mechanically and biochemically interacting cells (the “players” upon the stage). PhysiCell—physics-based multicellular simulator—is an open source agent-based simulator that provides both the stage and the players for studying many interacting cells in dynamic tissue microenvironments. It builds upon a multi-substrate biotransport solver to link cell phenotype to multiple diffusing substrates and signaling factors. It includes biologically-driven sub-models for cell cycling, apoptosis, necrosis, solid and fluid volume changes, mechanics, and motility “out of the box.” The C++ code has minimal dependencies, making it simple to maintain and deploy across platforms. PhysiCell has been parallelized with OpenMP, and its performance scales linearly with the number of cells. Simulations up to 105-106 cells are feasible on quad-core desktop workstations; larger simulations are attainable on single HPC compute nodes. We demonstrate PhysiCell by simulating the impact of necrotic core biomechanics, 3-D geometry, and stochasticity on the dynamics of hanging drop tumor spheroids and ductal carcinoma in situ (DCIS) of the breast. We demonstrate stochastic motility, chemical and contact-based interaction of multiple cell types, and the extensibility of PhysiCell with examples in synthetic multicellular systems (a “cellular cargo delivery” system, with application to anti-cancer treatments), cancer heterogeneity, and cancer immunology. PhysiCell is a powerful multicellular systems simulator that will be continually improved with new capabilities and performance improvements. It also represents a significant independent code base for replicating results from other simulation platforms. The PhysiCell source code, examples, documentation, and support are available under the BSD license at http://PhysiCell.MathCancer.org and http://PhysiCell.sf.net.", "link"=>"http://www.mendeley.com/research/physicell-open-source-physicsbased-cell-simulator-3d-multicellular-systems", "reader_count"=>53, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>1, "Researcher"=>14, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>12, "Student > Master"=>6, "Other"=>4, "Student > Bachelor"=>6, "Professor"=>2, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>1, "Researcher"=>14, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>12, "Student > Master"=>6, "Other"=>4, "Student > Bachelor"=>6, "Professor"=>2, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>6, "Engineering"=>2, "Biochemistry, Genetics and Molecular Biology"=>14, "Agricultural and Biological Sciences"=>11, "Medicine and Dentistry"=>2, "Neuroscience"=>2, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Physics and Astronomy"=>5, "Chemical Engineering"=>1, "Computer Science"=>7, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Neuroscience"=>{"Neuroscience"=>2}, "Physics and Astronomy"=>{"Physics and Astronomy"=>5}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>11}, "Computer Science"=>{"Computer Science"=>7}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>14}, "Unspecified"=>{"Unspecified"=>6}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Chemical Engineering"=>{"Chemical Engineering"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Spain"=>1}, "group_count"=>3}

Scopus | Further Information

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