Skip to content

Version 1.3.3
Compare
Choose a tag to compare
@MathCancer MathCancer released this 17 Sep 03:54
· 1569 commits to master since this release
1.3.3
8cb3c24

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

Version: 1.3.3
Release date: 16 September 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

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 introduces simplifications in versioning to facilitate
faster release cycles. It also introduces functions to register and
list citations for third-part add-ons. The goal is to encourage end-
users to properly cite PhysiCell and add-on products used in their
projects.

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

Major new features and changes:

  • none

Minor new features and changes:

  • Moved all version information to VERSION.txt to facilitate
    faster release cycles.

  • Updated all the Makefiles to set VERSION via

    VERSION := $(shell grep . VERSION.txt | cut -f1 -d:)

  • Moved detailed citation information to CITATION.txt to
    facilitate faster release cycles.

  • Changed std::string PhysiCell_version to
    std::string PhysiCell_Version for more consistency with
    prior BioFVM work.

  • Added new static string to PhysiCell.h:
    static std::string PhysiCell_DOI

  • Added new functions to PhysiCell_utilities to query
    PhysiCell versioning:

    std::string get_PhysiCell_version( void );

    void get_PhysiCell_version( std::string& pString );

  • Added the following function to PhysiCell_utilities to
    display a list of all software versions and citations
    used in the code:

    void display_citations( std::ostream& os );
    void display_citations( void );

    For example, use display_citations( std::cout ), or use
    an output file stream. Note that display_citations(void)
    calls display_citation(std::cout);

  • Updated all the sample projects to use display_citations();

Beta features (not fully supported):

  • Added ./protocols/ directory to include release and other
    instructions, to help train new developer contributors.
    Perhaps this should be called "checklists" ?

  • Added the following functions to PhysiCell_utilities to
    register third-party software citations in a global list,
    ready for query and display:

    void add_software_citation( std::string name ,
    std::string version, std::string DOI, std::string URL );

Bugfixes:

  • None

Notices for intended changes that may affect backwards compatibility:

  • We will probably move from README.txt to README.md to support
    markdown and improve releases on both SourceForge and GitHub.

  • We will probably move from changes.txt to changes.md to support
    markdown in the long-term change logs.

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

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. (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)

Assets 3
Loading