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

Version: 1.6.0

Release date: 20 August 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:

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 [project-name]: 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.

Release summary:

This release introduces a new XML-based configuration for the chemical microenvironment. All the sample projects have been updated to use this new functionality. There is no change in APIs or high-level usage / syntax for end users; old projects should continue to work without modification, although we highly recommend migrating to the simplified microenvironment setup. A short blog tutorial on this new functionality can be found at

http://mathcancer.org/blog/setting-up-the-physicell-microenvironment-with-xml

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

Major new features and changes:

  • XML-based setup of the chemical microenvironment.

Minor new features and changes:

  • Updated template2D sample project:

    • Refined "reset" and "data-cleanup" rules in Makefile
    • Converted project to use the new XML-based microenvironment setup.

  • Updated template3D sample project:

    • Refined "reset" and "data-cleanup" rules in Makefile
    • Converted project to use the new XML-based microenvironment setup.

  • Updated heterogeneity sample project:

    • Refined "reset" and "data-cleanup" rules in Makefile
    • Converted project to use the new XML-based microenvironment setup.

  • Updated cancer immune sample rpoject:

    • Refined "reset" and "data-cleanup" rules in Makefile
    • Converted project to use the new XML-based microenvironment setup.

  • Updated virus macrophage sample project:

    • Refined "reset" and "data-cleanup" rules in Makefile
    • Converted project to use the new XML-based microenvironment setup.
    • Enabled gradient calculations (were previously off, although we wanted macrophage chemotaxis)

  • Updated biorobots sample project:

    • Refined "reset" and "data-cleanup" rules in Makefile.
    • Converted project to use the new XML-based microenvironment setup.
    • Note that values in user_parameters will override values in microenvironment_setup.
    • Improved project to properly search for substrate indices instead of hard coding them.

  • Updated cancer biorobots sample project:

    • Refined "reset" rule in Makefile.
    • Converted project to use the new XML-based microenvironment setup.
    • Improved project to properly search for substrate indices instead of hard coding them.

  • Refined "reset" and "data-cleanup" rules in default Makefile

  • Created new function to access the (private) microenvironment dirichlet_activation_vector:

double Microenvironment::get_substrate_dirichlet_activation( int substrate_index );

  • Updated the main microenvironment display function Microenvironment::display_information to summarize the initial and boundary conditions for each substrate

  • Wrote two new functions to parse the XML in microenvironment_setup to add substrates and options:

    • bool setup_microenvironment_from_XML( pugi::xml_node root_node )
    • bool setup_microenvironment_from_XML( void ) The second one assumes you already defined the root node and access the global (pugi)xml node for it.

  • The main XML parsing function now calls setup_microenvironment_from_XML(), just before processing user-defined parameters.

Beta features (not fully supported):

  • anim_svg.py - now plots correctly sized cells; manually step via arrow keys

  • anim_svg_cycle.py - same as above, but automatically cycles through .svg files

Bugfixes:

  • None.

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