PhysiCell: PhysiCell: an Open Source Physics-Based Cell Simulator for 3-D
Multicellular Systems.
Version: 1.1.0
Release date: 16 May 2017
Homepage: http://PhysiCell.MathCancer.org
Downloads: http://PhysiCell.sf.net
Summary:
This release includes usability fixes and enhancements, including
more basic "template" projects, simpler project startup, improved SVG
visualization support, and cleanup on the Makefile.
PhysiCell is currently under scientific peer review.
Major new features and changes:
+ Added template3D.cpp and template2D.cpp template projects. See the
template_projects directory.
+ Added Makefile rules to seed the 2D projects. To create and compile
the 2D template:
make template2D && make
To create and compile the 3D template:
make template3D && make
To further edit your project, modify main.cpp in the root PhysiCell
directory. Follow the online tutorials for further functionality.
+ Added preliminary MultiCellDS support, with MultiCellDS outputs. These
are added via modules/PhysiCell_MultiCellDS.cpp
+ Many usability improvements listed in "minor new features" below.
+ Finished implementation of SVG support, to plot the simulation through a
cross-section (fixed z-value).
+ Digital pathology: Improved coloring functions for the main cell cycle
models, and virtual H&E (hematoxylin and eosin):
Minor new features and changes:
+ Created new function in PhysiCell_cell_container to simplify initialization
of the mechanics data structures:
Cell_Container* create_cell_container_for_microenvironment(
BioFVM::Microenvironment& m , double mechanics_voxel_size );
+ Usability feature: If BioFVM::default_microenvironment has not yet been
declared when calling create_cell_container_for_microenvironment(), then
it is set to "m" in the new function above.
+ Usability feature: If the BioFVM::default_microenvironment has been set
then Cell* create_cell( void ) now uses this to call
Cell::register_microenvironment(µenvironment).
+ Changed Cell_Parameters from a struct to a class.
+ Usability feature: Created a new Cell_Defaults class, with a
global PhysiCell::cell_defaults. Now, you can set these
default functions and parameters at the start of your program, and
all new cells are set to use these defaults.
+ Usability feature: Traced code and determined that calling Cell::set_phenotype()
calls Basic_Agent::set_total_volume() (Cell extends Basic_Agent), which sets
Basic_Agent::volume_is_changed to true. This, in turn, makes the next call
to Basic_Agent::simulate_secretion_and_uptake() call
Basic_Agent::set_internal_uptake_constants(). So, it is unnecessary to
call this function in typical initialization.
+ Usability feature: Cell:set_phenotype() now automatically calls
Basic_Agent::set_internal_uptake_constants(). You no longer need to
manually call this function *if* using the set_phenotype() function.
+ Usability feature: The default Cell constructor (Cell::Cell) uses
the default functions in PhysiCell::default_cell_functions, instead
of hard-coded defaults. The default constructor for Default_Cell_Functions
has sensible defaults for cell mechanics and volume regulation to
match the PhysiCell method paper. Phenotype-related functions are left
empty.
+ Usability feature: The create_cell() function now assigns the default
microenvironment to the newly created cell, and assigns the
cell functions in PhysiCell::default_cell_functions.
+ Changed default -march flag to -march=native, according to benchmarks
on gcc 5x at phoronix:
http://www.phoronix.com/scan.php?page=news_item&px=GCC-Optimizations-E3V5-Levels
+ Changed the -O3 flag to -Ofast, which tends to produce slightly faster
code by the phoronix link above.
+ Updated to a pre-release copy of BioFVM 1.1.5.
+ Included the matlab functions first created for BioFVM, which can now be
found in the matlab directory.
+ Fixed read_MultiCellDS_xml.m function to work when there are no cells.
+ Fixed read_MultiCellDS_xml.m function to display the current number of
cells, when there are < 3 cells.
+ Added modules/PhysiCell_standard_modules.h to start organizing non-core,
standard parts of MultiCellDS. This will inintially include SVG,
pathology, and MultiCellDS modules.
+ Removed matlab output from log_output in PhysiCell_utilities.cpp. This
only saved the microenvironment (but not cells), and it is no longer
needed with new MultiCellDS output support.
+ Changed the default SVG length scale bar in PhysiCell_pathology to
100 microns (previously 1000 microns).
+ Updated the archive rules to use the more-common "tar" command. Use
"make tar" and "make untar". Archives are stored in the archives
directory.
+ Added a void up_orientation( Cell* pCell, double dt ) to
PhysiCell_standard_models.cpp, which sets orientation = [0,0,1]
and polarity = 1.0. This is useful for 2-D simulations.
+ Digital Pathology coloring functions:
simple_cell_coloring: cell nucleus is blue, cytoplasm is red, and
outlines are black
false_cell_coloring_Ki67: for any Ki67-based cell cycle model,
green cells are Ki67+ prior to mitosis (or any Ki67+ cell in
the simplified Ki67 models), magenta cells are Ki67+ after
mitosis, red cells are apoptotic, and brown cells are necrotic.
hematoxylin_and_eosin_cell_coloring: "stains" nuclear solids with
hematoxylin, "stains" cytoplasmic solids with eosin, and simulates
light transmission / absorbtion through a thin slice to approximate
microscopy and image acquisition. Note that cells with little water
will appear dark (e.g., apoptotic debris, especially after the
cytoplasm has blebbed), and cells with lots of water (e.g., onsosis
in early necrotic cells) will appear faint.
false_cell_coloring_live_dead: live cells are green, apoptotic cells
are red, and necrotic cells are brown.
+ Added Phenotype::get_current_phase_code(void) to
PhysiCell_digital_cell_line.cpp to more easily get the cell's current
phenotypic state. (Especially useful for virtual pathology.)
Bugfixes and Corrections:
+ Fixed typo Time_Settings.cell_cylce_dt_default to
Time_Settings.cell_cycle_dt_default in PhysiCell_cell_container.
+ Removed unused declaration Cell::initialize_functions( void );
+ Changed the default "update_cell_and_death_parameters" function from
"update_cell_and_death_parameters_O2_based" to "empty_function".
Examples and models should choose this *explicitly*.
+ Cell::set_orientation( Cell* pCell ) changed to
Cell::set_orientation( Cell* pCell, double dt ) to be consistent with other
cell member functions.
+ In void Cell::assign_orientation(), set polarity = 0.0 if a
set_orientation(Cell*,double) function is not set (NULL).
+ Removed irrelevant data elements in the Custom_Cell_Data class.
Notices for intended changes that may affect backwards compatibility:
+ Will rename the current "Phenotype" class to "Full_Phenotype"
+ Will introduce a new Phenotype class with a much simpler structure.
+ Will rewrite the represetation of cell cycle and death phases.
+ Will rewrite the standard phenotype models in the simpler representatio.
+ Will stop requiring use of the Digital_Cell_Line class for initializing
simulations.
+ Will deprecate update_cell_and_death_parameters, and instead use
update_phenotype_parameters.
+ Will stop using the oxygen-dependent phenotype rule as default.
PhysiCell 1.1.0 includes an advance copy of BioFVM 1.1.5. Here are the changes:
/* fixes in BioFVM 1.1.5 */
+ correct typos in citation information in all source files
+ updated citation information
+ added void set_default_microenvironment( Microenvironment* M ) declaration to
BioFVM_Microenvironment.h
+ set volume_is_changed = false in Basic_Agent::set_internal_uptake_constants();
+ Set the MultiCellDS options Booleans to extern bool in BioFVM_MultiCellDS.h
so that PhysiCell can read these options.
+ Updated the simlified_data field in MultiCellDS XML output to include a
new "source" attribute with value "BioFVM".
Download Latest Version
PhysiCell_V.1.14.2.zip (12.4 MB)
