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PhysiCell: an Open Source Physics-Based Cell Simulator for 3-D
Release date: 23 February 2018
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.
Visit http://MathCancer.org/blog for the latest tutorials and help.
This release introduces two new cell cycle models (G0/G1 ->
S -> G2/M) and (G0/G1 -> S -> G2 -> M), introduces XML-based
configuration files, and allows new user control on how
often and where data are stored.
As usual, the release also contains minor bugfixes and
NOTE: OSX users must now define PHYSICELL_CPP system variable.
See the documentation.
Major new features and changes:
implemented new cell cycle models:
flow_cytometry_cycle_model: G0/G1 -> S -> G2/M
flow_cytometry_separated_cycle_model: G0/G1 -> S -> G2 -> M
along with documentation and updated coloring functions
The oxygen-based phenotype models now support the new cycle
Added XML file parsing for use in settings files.
XML configuration file (in ./config/PhysiCell_settings.xml)
sets data destination (as a subfolder) and save
frequency. Legacy saves are now off by default.
Users can select a different XML file at command line
(Assuming you preserved the structure of the template
Updated User_Guide to reflect new XML parsing capabilities.
Updated User_Guide to reflect new cell cycle models,
including reference parameters chosen for consistency with
the other cycle models.
Minor new features and changes:
Added PhysiCell_pugixml.* for easier extraction of parameter
arguments from XML files
Added PhysiCell_settings.* to include parsing of XML parameter
files, and parameter values stored in a unified data structure.
Added parsing of settings file to separately set frequency of
saving full output (MultiCellDS), SVG outputs, and "legacy"
outputs from USC era.
Added options to specify the folder of saved data.
Added option to read the number of OMP threads from a setting file.
Added "beta" directory where we will put new features that are still
Minor updates to the Quickstart guide.
Added new function: to display the simulation status:
void display_simulation_status( std::ostream& os );
e.g., display_simulation_status( std::cout );
writePov() uses a user-specified output folder.
log_output() uses a user-specified output folder.
added "beta-testing" sample project. Populate it by the rule:
added flow_cytometry_separated_cycle_model to the PhysiCell constants.
added G1pm_phase and G1ps_phase to the PhysiCell constants.
Added new coloring function: false_cell_coloring_cytometry
added support for the new cytometry cycle models to the oxygen-based
phenotype model (update_cell_and_death_parameters_O2_based)
updated user manual to reflect new cytometry models
updated template2D and template3D projects to use to use the
new cytometry models and coloring schemes. Also reduced to
1 mm x 1 mm (2D) and 1 mm^3 (3D) for faster demos.
removed archives directory
Beta features (not fully supported):
- XML functions moved from beta to production.
Changed instances of uniform_random() (from BioFVM) to
UniformRandom() (from PhysiCell) so that all calls to the PRNG
used the same random seed and same PRNG. Thanks, olliemcdonald!
Fixed typo in "Dirichlet" in user documentation. Thanks, luissv7!
Removed .git directory that was accidentally included in releases
(add_PhysiCell_cells_to_open_xml_pugi) so that we exit(-1) with a
meaningful error message if we cannot open a matlab subfile
Updated PhysiCell_pathology.cpp (SVG_plot) so that we exit(-1)
with a meaningful error message if we cannot open an SVG file
Notices for intended changes that may affect backwards compatibility:
- template_projects folder will be removed
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
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)