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

Versions: 1.13.0 -

Release dates: 29 July 2023 -

• 1.13.0 : 29 July 2023
• 1.13.1 : 6 August 2023

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.

Notable recognition:

• 2019 PLoS Computational Biology Research Prize for Public Impact

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:
  • template
  • biorobots-sample
  • cancer-biorobots-sample
  • cancer-immune-sample
  • celltypes3-sample
  • heterogeneity-sample
  • pred-prey-farmer
  • virus-macrophage-sample
  • worm-sample
  • ode-energy-sample
  • physiboss-cell-lines-sample
  • cancer-metabolism-sample
  • interaction-sample
  • mechano-sample
  • rules-sample
  • physimess-sample

make list-projects : list all available sample projects

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.

make save PROJ=name: save the current project (including the Makefile, main.cpp, and everything in ./config and ./custom_modules/) in ./user_projects/name, where name is your choice for the project. If the project already exists, overwrite it.

make load PROJ=name: load the user project name from ./user_projects/name (including the Makefile, main.cpp, and everything in ./config and ./custom_modules/).

make list-user-projects: list all user projects in ./user_projects/. (Use these names without the trailing / in make load PROJ=name.)

make jpeg : uses ImageMagick to convert the SVG files in the output directory to JPG (with appropriate sizing to make movies). Supply OUTPUT=foldername to select a different folder.

make movie : uses ffmpeg to convert the JPG files in the output directory an mp4 movie. Supply OUTPUT=foldername to select a different folder, or FRAMERATE=framerate to override the frame rate.

make upgrade : fetch the latest release of PhysiCell and overwrite the core library and sample projects.

Key Links

Homepage: http://PhysiCell.MathCancer.org

Downloads: http://PhysiCell.sf.net

Support: https://join.slack.com/t/physicellcomm-sf93727/shared_invite/zt-qj1av6yd-yVeer8VkQaNDjDz7fF00jA

Quick Start: Look at QuickStart.md in the documentation folder.

User Guide: Look at UserGuide.pdf in the documentation folder.

Setup and Training: See this year's workshop and hackathon at https://github.com/PhysiCell-Training/ws2023

Older Tutorials: http://www.mathcancer.org/blog/physicell-tutorials/

Latest info: follow @PhysiCell on Twitter (http://twitter.com/PhysiCell)

See changes.md for the full change log.

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Release summary:

Version 1.13.x introduces PhysiMeSS (MicroEnvironment Structures Simulation) as a PhysiCell add-on created to model rod-shaped microenvironment elements such as the matrix fibres (e.g. collagen) of the ECM. These releases also introduce numerous bug fixes, particularly to handling of Dirichlet boundary conditions, while introducing numerous minor feature enhancements such as packing and unpacking user projects (to facilitate code sharing).

Version 1.13.1 (6 August 2023):

Version 1.13.1 primarily introduces bug fixes for smoother addon support, as well as new makefile rules to pack a user project for sharing (make pack PROJ=name) and to unpack a shared project (make unpack PROJ=name). These will create (pack) or expand (unpack) zipped projects in the ./user_projects folder. To share, send the zipped file and encourage the recipient to store it in their own ./user_projects folder.

Version 1.13.0 (29 July 2023):

Version 1.13.0 introduces PhysiMeSS (MicroEnvironment Structures Simulation) as a PhysiCell add-on created by Cicely Macnamara, Vincent Noël and collaborators, which allows the user to specify rod-shaped microenvironment elements such as the matrix fibres (e.g. collagen) of the ECM. This allows the PhysiCell user the ability to investigate fine-grained processes between cellular and fibrous ECM agents. We are providing an sample project together with this addon to demonstrate, via many examples, the possibilities of PhysiMeSS. For more information, consult the PhysiMeSS README available in ./addons/PhysiMeSS/README.md. Version 1.13.0 also updates the bundled PhysiBoSS addon, introduces a variety of bug fixes (particularly in handling of Dirichlet boundary conditions), and improves SVG plots.

We are grateful for immense contributions by Cicely Macnamara, Vincent Noël, Randy Heiland, Daniel Bergman, Marco Ruscone, Furkan Kurtoglu, and Elmar Bucher in this release.

NOTE 1: MacOS users need to define a PHYSICELL_CPP environment variable to specify their OpenMP-enabled g++. See the Quickstart for details.

NOTE 2: Windows users need to follow an updated (from v1.8) MinGW64 installation procedure. This will install an updated version of g++, plus libraries that are needed for some of the intracellular models. See the Quickstart for details.

Major new features and changes in the 1.13.z versions

1.13.1

• None in this release

1.13.0

• Introduced PhysiMeSS, a major addon for modeling fibers of the extracellular matrix. Major thanks to Cicely Macnamara, Vincent Noël, and team!

Minor new features and changes:

1.13.1

• Continued modernization of sample projects for PhysiCell Studio compatibiltiy. See PR 198.
• Updated inhibitor behaviors in PhysiBoSS, and further code cleanup. See PR 194. Thanks, Marco Ruscone!
• PhysiBoSS cell line example migrated to newer MultiCellDS output. See PR 193. Thanks, Vincent Noël!
• Added a new makefile rule to simplify sharing user projects: make pack PROJ=name will zip all of the name user project in ./user_projects/name.zip. Send this zip file for sharing your project, and have your recipient:
  1. Place name.zip in thier ./user_projects/ folder (preferably PhysiCell version 1.13.1 or later)
  2. Have them run the new rule make unpack PROJ=name to expand the project.
  3. After this, the usual rules apply. make load PROJ=name to load the project, and a subsequent make to compile it.
• Added a new makefile rule to simplify use of shared user projects: make unpack PROJ=name will unzip the contents of ./user_projects/name.zip into a new user project called name. Type make load PROJ=name to load this project, and make to compile it.

1.13.0

• Preparations for a new derived Cell class for use in PhysiBoSS, including a new instantiate_cell function in Cell_Functions to help facilitate this. See PR 153 (Thanks, Vincent Noël!)
• Various safety refinements (const accessors) in vector operations (PR 160). Thanks, Vincent Noël!
• Made changes to cell SVG plotting to support broader types of plotting in advance of PhysiMeSS PR 162. Thanks, Vincent Noēl!
• Added a safe way to query the current velocity via Basic_Agent::get_previous_velocity() in preparation for PhysiMeSS. PR 163. Thanks, Vincent Noël!
• Refined control of object counts in SVG for upcoming PhysiMeSS release. PR 164. Thanks, Vincent!
• Refined SVG plot options to incorporate substrates. PR 181. Thanks, Marco Ruscone!
• Updated PhysiBoSS to Version 2.2.1. See PR 188. Thanks, Vincent Noël!
• Updated unit tests (including custom_DCs_2substrates)
• Added damage rate (from effector attack) to supported behaviors in the modeling gramamr
• minor cleanup

Beta features (not fully supported):

1.13.1

• The dFBA addon is considered "beta" and unsupported at this time. Compatability work is underway. Thank you, Miguel Ponce de Leon and team!

1.13.0

• None in this release.

Bugfixes:

1.13.1

• Bugfixes to and refinements to the libRoadrunner setup scripts. See PR 196. Thanks to Randy Heiland and Furkan Kurtoglu.
• Updated PHysiBoSS cell line example project to remove “default phenotype” function. See PR 195. Thanks, Vincent Noël!
• Fixed default cell constructor to improve backwards compatibility by including new SVG plot function pointers. See PR 200. Thanks to John Metzcar for catching this and for careful detective work to isolate the cause!
• Numerous bugfixes to PhysiCell zip distribution, including a better release protocol. Major thanks to Furkan Kurtoglu, Elmar Bucher, John Metzcar, and Randy Heiland for help!

1.13.0

• Fix typographical errors in Makefiles in sample projects.
• Set correct value (100) of cell_BM_repulsion_strength in PhysiCell_phenotype.cpp (Thanks, Elmar Bucher!)
• Improved handling of voxel_index in remove_agent_from_voxel in preparation for voxel-spanning objects such as PhysiMeSS. PR 159. Thanks, Vincent Noël!
• Fixed bug to ensure cell definitions without intracellular defined get a NULL intracellular model function. [PR 182](and PR 182. THanks, Marco Ruscone!
• Fixed a whitespaced bug in SVG output. PR 179. Thanks, Vincent Noël!
• Fixed a PhysiBoSS bug where dead cells could execute models. PR 180 Thanks, Vincent Noël!
• Fixed bugs involving Dirichlet conditions and multiple substrates (thanks to Daniel Bergman for pointing it out!) See [Issue 124](rf. MathCancer#124) and PR 149. Thank you, Daniel Bergman and Randy Heiland!
• cancer_biorobots Makefille PROGRAM_NAME is now cancer_biorobots instead of project
• Deleted a meaningless line dt; in PhysiCell_standard_models.cpp
• Added missing commas to cell_rules.csv in rules_sample project
• Fixed typo: PhyisiCell_rules.o to PhysiCell_rules.o in Makefile-default (thanks to Joseph Abrams for pointing it out!)
• Fixed errors in SBML ODE models. See PR 185 and PR 186. Thanks, Furkan Kurtoglu and Vincent Noël!
• Fixed errors the PhysiBoSS readme. See PR 187. Thanks, Vincent Noël!

Notices for intended changes that may affect backwards compatibility:

• We intend to deprecate the unused phenotype variables relative_maximum_attachment_distance, relative_detachment_distance, and maximum_attachment_rate from phenotype.mechanics.

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

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

• Additional search functions (e.g., to find a substrate or a custom variable) will start to return -1 if no matches are found, rather than 0.

• We will change the timing of when entry_functions are executed within cycle models. Right now, they are evaluated immediately after the exit from the preceding phase (and prior to any cell division events), which means that only the parent cell executes it, rather than both daughter cells. Instead, we'll add an internal Boolean for "just exited a phase", and use this to execute the entry function at the next cycle call. This should make daughter cells independently execute the entry function.

• We might make trigger_death clear out all the cell's functions, or at least add an option to do this.

• We might change the behavior of copied Custom Data when a cell changes type (changes to a new cell definition). Currently, all custom data elements in a cell are overwritten based on those in the new cell definition. This is not the best behavior for custom data elements that represent state variables instead of type-dependent parameters.

Planned future improvements:

• Further XML-based simulation setup.

• Read saved simulation states (as MultiCellDS digital snapshots)

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

• 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)

• Improved plotting options in SVG

• Further update sample projects to make use of more efficient interaction testing available

• Major refresh of documentation.