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@MathCancer MathCancer released this 24 Aug 12:07
· 1422 commits to master since this release
1.3.2
036cb18

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

Version: 1.3.2
Release date: 24 August 2018

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
URL: http://dx.doi.org/10.1371/journal.pcbi.1005991

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

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

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.txt for the full change log.

-=-=-=-=-

Release summary:

This release fixes a small gradient bug that I swear I had fixed before.

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 BioFVM, Microenvironment::compute_gradient_vector(int), removed "static"
    from "static std::vector indices(3,0)" to prevent rare segfaults.

  • In BioFVM, Microenvironment::compute_gradient_vector(int), replaced "static"
    for "bool gradient_constants_defined = false". Yep, I removed static from
    the wrong line in 1.3.1

  • Correct some errors in both the README.txt and changes.txt files.

Notices for intended changes that may affect backwards compatibility:

  • None.

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 https://doi.org/10.1101/267070.)

  • Develop contact-based cell-cell interactions. (Likely in next release.)

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

  • 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)

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