PhysiCell: an Open Source Physics-Based Cell Simulator for 3-D
Multicellular Systems.
Version: 1.2.2
Release date: 4 November 2017
Overview:
PhysiCell is a flexible open source framework for building
agent-based multicellular models in 3-D tissue environments.
Reference: Ghaffarizadeh et al., PLoS Comput Biol (2017)
preprint URL: https://doi.org/10.1101/088773
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 <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
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.
Summary:
This release reduces the complexity of Makefiles (especially for
OSX users), restructures the 2D and 3D project templates as
sample projects, fixes a minor bug in SVG pathology outputs,
improves copying of Cell_Definitions, and fixes minor bugs in
BioFVM (primarily related to Dirichlet conditions).
NOTE: OSX users must now define PHYSICELL_CPP system variable.
See the documentation.
PhysiCell is currently under scientific peer review.
Major new features and changes:
+ none
Minor new features and changes:
+ Restructured the 2D template project to have the same structure as a
typical project, with setup functions related functions in
./custom_modules/*, etc. Moved it to ./sample_projects/template2D/
./template_projects/ will be deprecated.
To populate this project, use:
make template2D
To compile:
make
To de-populate the sample project and return to the "clean"PhysiCell state:
make reset
make clean (to remove object files)
+ Restructured the 3D template project to have the same structure as a
typical project, with setup functions related functions in
./custom_modules/*, etc. Moved it to ./sample_projects/template3D/
./template_projects/ will be deprecated.
To populate this project, use:
make template3D
To compile:
make
To de-populate the sample project and return to the "clean"PhysiCell state:
make reset
make clean (to remove object files)
+ Simplified Makefiles: populating a sample project and compiling it
make <sample_project>
To compile:
make
To reset to original state:
make reset
Current <sample_project> values:
template2D
template3D
biorobots-sample
cancer-biorobots-sample
heterogeneity-sample
cancer-immune-sample
+ Simplified Makefiles: Makefiles check for system variable
PHYSICELL_CPP to set the compiler (CC). OSX users must set
this environment variables. See the online tutorials and the
user guide.
+ Simplified Makefiles: "make data-cleanup" removes .svg, .mat, .xml, and
data inside ./data
+ Updated documentation on how to add new substrates.
+ Updated documentation on applying Dirichlet conditions to only
specific substrates.
+ Added new function to copy the properties of a Cell Definition to
the cell.
void Cell::convert_to_cell_definition( Cell_Definition& cd )
Bugfixes:
+ Fixed a small error in SVG plots, where tissues were flipped with
y was vertically flipped.
+ Used register_microenvironment(Microenvironment*) to improve
compatibiltiy with other operating systems and compilers.
+ Added copy constructor and copy assignnment functions to the
Cell_Definition is.
+ Removed the unnecessary "wha???" from BioFVM_microenvironment.cpp.
+ Updated Dirichlet_condition_vector = ones (instead of zeros) in
Microenvironment_Options::Microenvironment_Options() default
constructor.
+ Microenvironment::resize_densities( int new_size ) no longer
overwrites previous dirichlet values when extending the size.
+ No longer overwrites existing Dirichlet_condition_vector elements
or set default_microenvironment_options.use_oxygen_as_first_field
to false.
+ Microenvironment::set_density(int,std::string,std::string) and
Microenvironment::set_density(int,std::string,std::string,double,double)
were modified to be compatibility.
+ Only set default_microenvironment_options.use_oxygen_as_first_field = false
if index = 0, when samplign the oxygen.
+ Updated save_PhysiCell_to_MultiCellDS_xml_pugi() to save much more
phenotype information and all custom variables for each cell.
+ Updated read_MultiCellDS_XML.m (in ./matlab) to read these
newly expanded data files.
+ Includes a sneak preview of BioFVM 1.1.7, which includes bugfixes
mentioned above.
Notices for intended changes that may affect backwards compatibility:
+ None at this time
Planned future improvements:
+ parse XML configuration files
+ 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
+ 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)
Download Latest Version
PhysiCell_V.1.14.2.zip (12.4 MB)
