PhysiCell: an Open Source Physics-Based Cell Simulator for 3-D Multicellular Systems.

Version: 1.5.1

Release date: 7 June 2019

Overview:

PhysiCell is a flexible open source framework for building agent-based multicellular models in 3-D tissue environments.

Reference: A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellular Systems, PLoS Comput. Biol. 14(2): e1005991, 2018. DOI: 10.1371/journal.pcbi.1005991

Visit http://MathCancer.org/blog for the latest tutorials and help.

Notable recognition:

• 2019 PLoS Computational Biology Research Prize for Public Impact

Key makefile rules:

make : compiles the current project. If no project has been defined, it first populates the cancer heterogeneity 2D sample project and compiles it

make : populates the indicated sample project. Use "make" to compile it.

<project_name> choices: template2D template3D biorobots-sample cancer-biorobots-sample heterogeneity-sample cancer-immune-sample virus-macrophage-sample

make clean : removes all .o files and the executable, so that the next "make" recompiles the entire project

make data-cleanup : clears out all simulation data

make reset : de-populates the sample project and returns to the original PhysiCell state. Use this when switching to a new PhysiCell sample project.

Homepage: http://PhysiCell.MathCancer.org

Downloads: http://PhysiCell.sf.net

Support: https://sourceforge.net/p/physicell/tickets/

Quick Start: Look at QuickStart.pdf in the documentation folder.

User Guide: Look at UserGuide.pdf in the documentation folder.

Tutorials: http://www.mathcancer.org/blog/physicell-tutorials/

Latest info: follow @MathCancer on Twitter (http://twitter.com/MathCancer)

See changes.md for the full change log.

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Release summary:

This minor release fixes bugs in the new virus-macrophage sample project. Users should also consult the reslease notes for 1.5.0.

NOTE: OSX users must now define PHYSICELL_CPP system variable. See the documentation.

Major new features and changes:

• None

Minor new features and changes:

• None

Beta features (not fully supported):

• None

Bugfixes:

• In the virus-macrophage sample project, switch cell death (in epithelial_function) from apoptosis to cell_lysis to demonstrate the new function.

• In the virus-macrophage sample project, enable internalized substrate tracking in the setup_microenvironment() function.

• In the virus-macrophage sample project, use a slower viral replication rate. (Should take 240 minutes to reach the lysis threshold.)

• In the virus-macrophage sample project, switched to a maximum simulation time of 24 hours (1440 minutes).

Notices for intended changes that may affect backwards compatibility:

• We intend to merge Custom_Variable and Custom_Vector_Variable in the very near future.

• We may change the role of operator() and operator[] in Custom_Variable to more closely mirror the functionality in Parameters.

• We will introduce improvements to placement of daughter cells after division.

• Some search functions (e.g., to find a substrate or a custom variable) will start to return -1 if no matches are found, rather than 0.

Planned future improvements:

• Further XML-based simulation setup.

• read saved simulation states (as MultiCellDS digital snapshots)

• "mainline" prototype cell attach/detach mechanics as standard models (currently in the biorobots and immune examples)

• integrate SBML-encoded systems of ODEs as custom data and functions for molecular-scale modeling

• integrate Boolean network support from PhysiBoSS into the mainline code (See http://dx.doi.org/10.1093/bioinformatics/bty766. )

• Develop contact-based cell-cell interactions.

• Add cell differentiation functionality to Phenotype, to be executed during cell division events.

• Add a new standard phenotype function that uses mechanobiology, where high pressure can arrest cycle progression. (See https://twitter.com/MathCancer/status/1022555441518338048.)

• Add module for standardized pharmacodynamics, as prototyped in the nanobio project. (See https://nanohub.org/resources/pc4nanobio.)

• create an angiogenesis sample project

• create a small library of angiogenesis and vascularization codes as an optional standard module in ./modules (but not as a core component)

• improved plotting options in SVG

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