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)