Version 1.4.1

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

Version: 1.4.1
Release date: 2 October 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.md for the full change log.

---

Release summary:

This release improves includes minor bug fixes for compiling in older versions of MinGW, and simplified XML MultiCellDS outputs that no longer record the relative pathing to .mat files. (This allows users to read data from their actual locations, rather than from a parent directory.) This release includes minor code cleanups in BioFVM for cleaner compiling in Ubuntu. Lastly, we have make small refinements to the sample projects and makefiles to default data saving to the ./output directory, and to prevent future releases from excluding the output directory from the zip releases.

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

Major new features and changes:

• None

Minor new features and changes:

• Changed the MultiCellDS outputs to only store the filename, and not the full relative path, in the tags. This makes it simpler to load MultiCellDS outputs from matlab and other platforms. (No longer need to read from a directory higher up to make the relative pathing correct.)

• Did major cleanup on BioFVM so that it compiles cleanly on Ubuntu.

• All sample projects output to the ./output directory

Beta features (not fully supported):

• None

Bugfixes:

• Updated the Parameter constructor functions to create a specialized version for std::string, to fix odd compiling bugs on older versions of MinGW. (Worked in 7.1.0, but not in 5.3.0.) Now, Parameter for T = bool, int, or double get initialized to value = (T) 0. And Parameter for T = std::string gets initialized to "none". I had hoped to do a unified version, but value = (T) 0 for std::string acts like a NULL pointer.

• All Makefiles ensure that the reset and data-cleanup rules leave at least empty.txt in ./output, so that future releases are never missing the output directory.

Notices for intended changes that may affect backwards compatibility:

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

• We may change the role of operator() and operator[] in Custom_Variable to more closely mirror the functionality in Parameters.

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 cell differentiation functionality to Phenotype, to be executed during cell division events.

• Add a new standard phenotype function that uses mechanobiology, where high pressure can arrest cycle progression. (See https://twitter.com/MathCancer/status/1022555441518338048.)

• 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)

• (optionally) track internalized substrate, coupled with BioFVM

Version 1.4.0

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

Version: 1.4.0
Release date: 26 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 improves the use of XML parsing in configuring simulations, notably (1) reading the domain parameters instead of hard-coded values, and (2) parsing a <user_parameters> block in the XML config files to populate a global parameters data structure of Boolean, integer, double, and std::string variables. Users can efficiently query these from within any function anywhere in a PhysiCell project.

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

Major new features and changes:

• User Parameters!

• Parsing XML to set domain size for all sample projects.

Minor new features and changes:

• Updated all the sample projects to use the improved XML parsing;

• New functions in PhysiCell_pugixml:

  1. std::string xml_get_my_name( pugi::xml_node node );

     This helps to easily extract the name of an XML node. (e.g., returns bob.)

  2. bool xml_get_my_bool_value( pugi::xml_node node );

     This gets the Boolean value of an XML node. (e.g., true returns true.)

  3. int xml_get_my_int_value( pugi::xml_node node );

     This gets the integer value of an XML node. (e.g., 42 returns 42.)

  4. double xml_get_my_double_value( pugi::xml_node node );

     This gets the double value of an XML node. (e.g., 42.03 returns 42.03.)

  5. std::string xml_get_my_string_value( pugi::xml_node node );

• Updated all Makefiles to copy main.cpp, the Makefile, and ./config/PhysiCell_settings.xml to backup copies prior to populating any sample project.

• Updated the heterogeneity sample project:

  1. Use the domain settings from the XML config file

  2. Use the XML config file options to set the initial tumor size and oncoprotein distribution.

  3. Get the random seed from the XML config file.

  4. Rewrote the custom coloring function to scale from min oncoprotein value (blue) to max oncoprotein value (yellow).

• Updated template2D sample project:

  1. Use the domain settings from the XML config file

  2. Use the XML config file to set the motile cell parameters

  3. Get the random seed from the XML config file.

  4. Updated to use the my_coloring_function coloring function. Made sure the my_coloring_function used false_cell_coloring_cytometry as its starting point.

• Updated template3D sample project:

  1. Use the domain settings from the XML config file

  2. Use the XML config file to set the motile cell parameters

  3. Get the random seed from the XML config file.

  4. Updated to use the my_coloring_function coloring function. Made sure the my_coloring_function used false_cell_coloring_cytometry as its starting point.

• Updated biorobots sample project:

  1. Use the domain settings from the XML config file

  2. Use the XML config file to set parameters and colors throughout the biorobots.cpp file

  3. Get the random seed from the XML config file

• Updated cancer immune sample project:

  1. Use the domain settings from the XML config file

  2. Use the XML config file to set parameters throughout the cancer_immune_3D.cpp file

  3. Get the random seed from the XML config file

• New function in ./core/PhysiCell_utilities:

  int choose_event( std::vector );

  If probabilities is a vector of n probabilities (for n events), and the sum of the probabilities is 1, then this chooses one of those n events according to these probabilities and returns the index of the selected event.

• Moved from README.txt to README.md to support markdown and improve releases on both SourceForge and GitHub.

• Moved from changes.txt to changes.md to support markdown and improve releases on both SourceForge and GitHub.

Beta features (not fully supported):

• None

Bugfixes:

• Updated the "reset" rules so that the default config file is restored (in all the sample makefiles).

• Removed a cout from Mechanics::set_relative_equilibrium_distance() from ./core/PhysiCell_phenotype.*

Notices for intended changes that may affect backwards compatibility:

• 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 cell differentiation functionality to Phenotype, to be executed during cell division events.

• Add a new standard phenotype function that uses mechanobiology, where high pressure can arrest cycle progression. (See https://twitter.com/MathCancer/status/1022555441518338048.)

• 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)

Version 1.3.3

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)

Version 1.3.2

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

Version: 1.3.2
Release date: 24 August 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
URL: http://dx.doi.org/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 fixes a small gradient bug that I swear I had fixed before.

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

Major new features and changes:

• none

Minor new features and changes:

• none

Beta features (not fully supported):

• none

Bugfixes:

• In BioFVM, Microenvironment::compute_gradient_vector(int), removed "static"
  from "static std::vector indices(3,0)" to prevent rare segfaults.

• In BioFVM, Microenvironment::compute_gradient_vector(int), replaced "static"
  for "bool gradient_constants_defined = false". Yep, I removed static from
  the wrong line in 1.3.1

• Correct some errors in both the README.txt and changes.txt files.

Notices for intended changes that may affect backwards compatibility:

• None.

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 https://doi.org/10.1101/267070.)

• 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)

Version 1.3.1

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

Version: 1.3.1
Release date: 31 July 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
URL: http://dx.doi.org/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 a new cycle model with an active cycling state and a quiescent state. It also adds new functions to the Mechanics class to make it easier to modify the cell-cell interaction distance (while maintaining equilibrium cell-cell spacing), or to modify the equilibrium cell-cell spacing. The release also includes major reliability and performance improvements to how gradients are calculated.

As usual, the release also contains minor bugfixes and improvements.

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

Major new features and changes:

• Implemented a new cell cycle model (cycling_quiescent),
  where quiescent cells can enter a cycling state. This
  model uses identical parameters to the Ki67-basic cycle
  model, but decouples the conceptual model from Ki67
  immunohistochemistry.

  Updated the documentation and coloring functions accordingly.

  Updated update_cell_and_death_parameters_O2_based() to
  support the new cycling_quiescent cycle model.

• update_all_cells(t,dt,dt,dt) now checks to see if gradient
  calculations are enabled, and if so, computes it once per dt_mechanics.

  This improves code performance by 2x to 3x in gradient-enabled codes,
  because we no longer need to calculate gradients once per dt_diffusion
  time step. (Gradients are only needed for cell velocity calculations,
  and occasionally for phenotype decisions.)

  All sample projects have been updated to make use of this.

  Also, removed the explicit gradient calculations from the template
  and sample projects.

• Added a new function to Mechanics class to simplify changes to cell
  interaction distances:

  void set_relative_maximum_adhesion_distance( double new_value );

  Here, new_value is a multiple of the cell's (mean equivalent) radius.
  Our default is 1.25. This function preserves the cell's "repulsion"
  strength and adjusts the strength of cell-cell adhesion to maintain
  its prior equilibrium cell-cell spacing.

• Added a new function to Mechanics class to simplify changes to cell
  equilibrium distances.

  void set_relative_equilibrium_distance( double new_value );

  Here, new_value is a multiple of the cell's (mean equivalent) radius.
  The default is around 1.9. This function preserves the cell's "repulsion"
  and the maximum interaction distance, and it adjusts the strength of
  cell-cell adhesion to match the new equilibrium cell-cell spacing.

  Note that this function performs a "sanity check" to ensure that you have
  not given a value greater than 2.0.

• Added a new function to Mechanics class to simplify changes to cell
  equilibrium distances.

  void Mechanics::set_absolute_equilibrium_distance( Phenotype& phenotype,
  double new_value )

  Here, new_value is the new equilibrium spacing (in units of microns).
  The function internally requires the cell's mean equivalent radius,
  and so you pass the cell's phenotype (by reference) as an additional
  argument.

  Note that this function performs a "sanity check" to ensure that you have
  not given a value greater than 2.0 * mean_cell_radius.

  Also note that PhysiCell internally uses a relative spacing, so the
  absolute spacing will change from the value you set, over time.

• Updated User_Guide to reflect new cell cycle model,
  including reference parameters chosen for consistency with
  the other cycle models.

Minor new features and changes:

• Added the following constants to support the new cycle model

  static const int cycling = 17;
  static const int quiescent = 18;
  static const int cycling_quiescent_model = 7;

• Removed the (never-used) Mechanics.maximum_adhesion_distance.

• Removed the legacy template_projects folder.

Beta features (not fully supported):

• Added a function pointer to the Cell_Functions class for intended
  contact-based cell-cell interaction, like delta-Notch signaling.

  void (contact_function)(Cell pMyself, Phenotype& my_phenotype,
  Cell* pOther, Phenotype& other_phenotype, double dt );

  It would be up to the user to define these functions and decide
  if the functions modify pMyself, pOther, or both. For now,
  the code will initialize the pointer to NULL and won't use it.

• Open to comments on handling cell-cell contact functions. Here's what
  I have in mind:

  notation: cell i interacts with cell j with function f(i,j).

  Each cell agent can hold one contact-based interaction function f,
  to be stored as a pointer in the cell's instance of the Cell_Functions
  class.

  We use the containers (and their interaction testing structures) to
  identify all interactions (i,j,f), and add it to a vector of interactions.
  The interaction (i,j,f) is added to the list so long as (j,i,f) is not
  already in the list, to avoid double-counting the interaction.

  The code will seek through the "container" interaction testing
  data structure, probably at the cell mechanics time scale, and update /
  recreate the vector of contact-based interactions (i,j,f).

  The code would likely go through the vector of interactions and
  execute the codes once per dt_diffusion time step, since I would
  imagine molecular biology (with faster time scales) is intended here.

  Since f(i,j) can potentially modify both cell i and cell j, it's probably
  not thread-safe. So we'll probably need that in a non-parallel loop.

  We will probably add a new time scale for interactions, dt_interactions,
  and update the interaction list on that time scale.

  For faster checking if (i,j,f) or (j,i,f) is already in the vector,
  we'll probably want some sort of hash map in addition to the vector
  of interactions.

  We'll probably implement this all in something like
  PhysiCell_contact_interctions.*, and add a global enable/disable option.
  I'd imagine we'd add code to the "update_all_cells" to keep this
  as simple to the users as possible.

  We should probably update each cell's "neighbors" data structure at
  when we're doing all this testing.

  In a longer-term update, we could leverage that for simpler interaction
  testing during velocity updates.

Bugfixes:

• Added missing "omp_set_num_threads(PhysiCell_settings.omp_num_threads)"
  in the main-heterogeneity.cpp file for the heterogeneity sample project.

• In BioFVM, Microenvironment::compute_gradient_vector(int), removed "static"
  from "static std::vector indices(3,0)" to prevent rare segfaults.

• Changed root above the comment lines in output files for
  better Python parsing compatibility. Thanks, rheiland!

Notices for intended changes that may affect backwards compatibility:

• None.

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 https://doi.org/10.1101/267070.)

• 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....

Version 1.3.0

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

Version: 1.3.0
Release date: 23 February 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.

Summary:
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
improvements.

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
  model.

• 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

  ./project_name settings_file.xml

  (Assuming you preserved the structure of the template
  projects.)

• 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
  undergoing testing

• 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:
  make beta-testing

• 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.

Bugfixes:

• 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

• Updated PhysiCell_MultiCellDS.cpp
  (add_PhysiCell_cells_to_open_xml_pugi) so that we exit(-1) with a
  meaningful error message if we cannot open a matlab subfile
  for writing.

• Updated PhysiCell_pathology.cpp (SVG_plot) so that we exit(-1)
  with a meaningful error message if we cannot open an SVG file
  for writing.

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)

Version 1.2.2

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)

Version 1.2.1

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

Version: 1.2.1
Release date: 1 September 2017

Homepage: http://PhysiCell.MathCancer.org
Downloads: http://PhysiCell.sf.net

Summary:
This release introduces a improved MultiCellDS outputs, new matlab
functions to read the MultiCellDS outputs, experimental functions
for povray routines (for 3-D raytracing), some bugfixes, and
new sample projects in cancer heterogeneity, synthetic multicellular
bioengineering, and cancer immunology.

PhysiCell is currently under scientific peer review.

Major new features and changes:

• 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.

• Included new matlab functions for fast 3-D data exploration:

  simple_plot.m -- quickly plots (as a surface) all the cells
  simple_cutaway_plot.m -- same as above, but with a cutaway view
  composite_cutaway_plot.m -- plots cutaway view of live and dead
  cells, colored separately.

• Wrote new POV-ray functions for future raytracing utilities. See
  ./modules/PhysiCell_POV.*

• Add the following new sample projects:

  biorobots: simulates a system of director, worker, and cargo
  cells that coordinate to deliver cellular cargo to the
  directors. Uses motility, custom mechanics, and other functions.

   build via: make biorobots-sample && make project 
  

  cancer biorobots: modifies the above project so that worker
  cells take cargo to hypoxic tumor regions. cargo cells
  release a drug once they are detached from worker cells.
  tumor cells have a damage and apoptosis model.

   build via: make cancer-biorobots-sample && make project 
  

  heterogeneity: simulates proliferation of a heterogeneous
  tumor. Note the loss of symmetry and selection/evolution.

   build via: make heterogeneity-sample && make project 
  

  cancer immunology: simulates an immune system attack on a
  tumor with heterogeneous proliferation and immunogenicity
  characteristics. In 3D!

   build via: make cancer-immune-sample && make project 
  

Minor new features and changes:

• Added double NormalRandom( double mean, double standard_deviation )
  to PhysiCell_utilities.* This will generate normally-distributed
  random numbers.

• Includes a sneak preview of BioFVM 1.1.7, which includes bugfixes on
  how boundary conditions were initialized.

bugfixes:

• Removed annoying "cout" lines in:

  void standard_live_phase_entry_function(Cell*,Phenotype&,double).

  They were leftover from debugging. Sorry!

• In the templates, we updated to:

    while( t < t_max + 0.1*diffusion_dt )
    {
  

  so that the simulations run all the way to the final time,
  instead of exiting too early by dt time.

• Fixed a bug in Motility::Motility() where the migration bias was
  initialized to (1,0,0).

• Made adhesion and repulsion symmetric across cells (in add_potentials)

• got rid of debug_temp_a in (in add_potentials)

• if default_microenvironment_options.simulate_2D == true, we now
  set velocity[2] = 0.0 in the velocity functions.

Version 1.2.0

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

Version: 1.2.0
Release date: 30 July 2017

Homepage: http://PhysiCell.MathCancer.org
Downloads: http://PhysiCell.sf.net

Summary:
This release introduces a major reworking to simplify cell pheno-
types and cells. It includes a generalized cell cycle model that
can also be used to represent death cycle models. It includes an
improved motility representation. Changing cell secretion and
uptake rates is more straightforward, because all interfacing
with BioFVM is automated.

A new, comprehensive user guide is included on all the major
functions and classes in PhysiCell, including examples.

This release also includes bugfixes and corrections. Due
to the extensive redevelopment, this change log is not 100%
fine-grained.

PhysiCell is currently under scientific peer review.

Major new features and changes:

• Completely reworked the Phenoytype class to be much more
  straightforward, and safe to change throughout the
  simulation.

• The Phenotype class includes elements on cell cycling, death,
  volume, geometry, mechanics, motility, and secretion (and uptake).

• Completely reworked representation of cell cycle models as
  Cycle_Model: a directed graph of Phases, linked by Phase_Links.
  A Cycle_Model is bundled with key parameters (Cycle_Data) into
  the Cycle element of the Phenotype.

• Cycle models can include user-specified arrest functions between
  Phases (e.g., contact inhibition).

• Cycle Phases can have user-specified "entry" and "exit" functions
  to be executed upon entering or leaving a Phase (e.g., mutations).

• Created new classes Death_Parameters and Death to represent
  cell death models as Cycle_Model.

• Updated the classes for Mechanics, Volume, and Geometry.

• Completely reworked the Motility class to represent cell
  migration as a combination of random and directed motility.
  Notions of persistence time are included. Users can supply
  custom functions to update the cell's migration bias.

• Added the cell calcification model to the general volume update
  function.

• Deprecated all code in core/PhysiCell_digital_cell_line.*

• Added apoptosis_death_model, necrosis_death_model,
  autophagy_death_model, and live_cells_cycle_model to
  PhysiCell_Constants.

• Added new function Cell::flag_for_division() for simpler
  construction of cycle models, and to allow users to push a cell
  to divide at any time.

• Added new function Cell::flag_for_removal() for simpler
  construction of cycle models, and to allow users to push a cell
  to be removed at any time.

• Volume::multiply_by_ratio() now also divides the target volumes by
  this ratio.

• Created a new Cell_Functions class to more readily bundle the
  Cell object's function pointers.

• Rewrote the Custom_Cell_Data class, so that custom data are no
  longer hard-coded by the user in the class, but instead added
  during runtime. Moved PhysiCell_custom.h/cpp into the core
  directory.

• The Cell_Definition class includes a pointer to the default
  Microenvironment, as well as a default Cell_Functions,
  Cell_Parameters, Custom_Cell_Data, and Phenotype. Newly created
  cells all copy from the Cell_Defaults.

• Bundled the following phenotype update functions into a single
  Phenotype::advance_all_nonmechanics_models( Cell* , double )
  function:
  Phenotype::update_function() // update cell phenotype parameters
  Phenotype::volume.update() // update cell volume
  Phenotype::geometry.update() // update radius, etc.
  Phenotype::death.check_for_death() // check for death
  Phenotype::cycle.advance_cycle() // advance the current cycle model

• PhysiCell_Container uses the above function on each cell to
  ensure that the correct custom functions are used. It also uses
  the cell's Cell::Cell_Functions::update_velocity() to update
  the cell's state. For now, users need to remember to include
  the motility update functions in their update_velocity() function
  if they replace the default. Lastly, PhysiCell_Container calls teh
  Cell::Cell_Functions::custom_cell_rule at the end of the main loop.

• Created new functions to directly trigger cell death.

• Created new functions to access cell neighbor information.

• Updated the examples for compatibility.

Minor new features and changes:

• Added PhysiCell_constants::custom_phase to the constants.

• Changed Cell:is_movable to Cell_is_movable to better express its
  purpose of setting a cell to rigid (unmovable) or movable.

• Fixed Cell:turn_off_reactions(double) to completely turn off all
  BioFVM uptake/secretion, rather than cut them by an order of
  magnitude.

• Replaced scores of (if some_double == 0) conditionals with
  if( fabs( some_double ) < tolerance ), since you it is best practice
  to never check for equality of a floating point or double.

• Started substituting more efficient axpy and += operators
  (from BioFVM) for many of the vector operations in PhysiCell_cell.cpp.

• Where possible, inserted { } into if / then / else logic for
  increased code clarity and robustness to newline and whitespace
  changes.

• Moved most default / standard mechanics functions from PhysiCell_cell.* to
  PhysiCell_standard_models.*.

• Added constants for time step sizes, time units, and spatial units to
  PhysiCell_constants.h, and removed isolated (and sometimes non-
  synchronized) timestep constants throughout the code.

• Added State::simple_pressure for future use in mechanics-induced cycle
  regulation.

• Added std::vector<Cell*>& Cell:cells_in_my_container(void) to more
  easily access a list of cells in the cell's current mechanics voxel.

• and more.

• Simplified the Makefile for easier cross-platform compiling. Users
  do not need to change MARCH any more.

Bugfixes and Corrections:

• Fixed typo "max_cell_interactive_ditstance_in_voxel" to
  "max_cell_interactive_ditstance_in_voxel" in the Cell_Container class.

• Throughout the code, replaced any logic of the form
  (if some_double == some_other_double ) with better practice of
  if( fabs( some_double - some_other_double ) < tolerance ), since
  floating point numbers aren't often equal.

• In PhysiCell_cell_container, the function find_escaping_face_index()
  had a return type of int, but it was possible for none of the statements
  to evaulate "true". The function now returns -1 for the case that
  there is no escaping_face_index. Thus, the return type is always defined.

• Cell::assign_position() now sets:
  is_out_of_domain = true;
  is_active = false;
  is_movable = false;
  if the cell is out of bounds. This should prevent segfaults when cells
  are assigned positions out of bounds (e.g., during division).

• Cell::update_position() now sets:
  is_out_of_domain = true;
  is_active = false;
  is_movable = false;
  if the cell moves out of bounds. This should prevent segfaults when cells
  move out of bounds (e.g., by mechanics).

Version 1.1.1

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

Version: 1.1.1
Release date: 18 May 2017

Homepage: http://PhysiCell.MathCancer.org
Downloads: http://PhysiCell.sf.net

Summary:
This release includes minor bugfixes and corrections.

PhysiCell is currently under scientific peer review.

Major new features and changes:

• none

Minor new features and changes:

• none

Bugfixes and Corrections:

• Changed "#include "../biofvm/BioFVM_MultiCellDS.h" to
  #include "../BioFVM/BioFVM_MultiCellDS.h" in modules/PhysiCell_MultiCellDS.h
  to fix compile errors. (Thanks, Randy Heiland!)

• Replaced instances of "kid" to the more customary "child" (parent and child
  objects) in core/PhysiCell_cell.cpp

• Modified the "make clean" rule in the Makefile to work better across
  platforms. (Previously worked fine on the object files, but only deleted
  $(PROGRAM_NAME).exe on Windows platforms.

• Modified the "template2D" and "template3D" rules in the Makefile to
  copy the current Makefile to template_projects/Makefile.backup

• Corrected the comments in template2D.cpp and template3D.cpp to more
  accurately note that we are seeding the three initial cells in all the
  states of the Ki67 advanced model. (Ki67+ premitotic, Ki67+ postmitotic,
  and Ki67-).

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
  representation.

• 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.

---

---

Version: 1.1.1
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(&microenvironment).

• 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 1.1.1 includes an advance copy of BioFVM 1.1.5. Here are the changes:

/* fixes in Bi...