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Recent news

Tuesday, Sep 19th, 2017
Working with PhysiCell MultiCellDS digital snapshots in Matlab: PhysiCell 1.2.1 and later saves data as a specialized MultiCellDS digital snapshot, which includes chemical substrate fields, mesh information, and a readout of the cells and ... [read more]

Sunday, Sep 3rd, 2017
Common problems and solutions: Here, we document common problems and solutions in compiling and running PhysiCell projects. Compiling Errors I get the error “clang: error: unsupported option ‘-fopenmp’” when I compile ... [read more]

Click here for more news!

PhysiCell: an open source physics-based cell simulator

Download the latest version (1.2.1)

Introduction

Many multicellular systems problems can only be understood by studying how cells move, grow, divide, interact, and die. Tissue-scale dynamics emerge from systems of many interacting cells as they respond to and influence their microenvironment. The ideal "virtual laboratory" for such multicellular systems simulates both the biochemical microenvironment (the "stage") and many mechanically and biochemically interacting cells (the "players" upon the stage). PhysiCell was developed to work in concert with BioFVM to fill this role as a virtual laboratory.

Project goals

PhysiCell aims to provide a robust, scalable code for simulating large systems of cells in 3-D tissues on standard desktop computers. Among our design goals:

What's New Back to top

September 1, 2017: We released PhysiCell 1.2.1, which includes four major new sample projects in multicellular bioengineering, cancer heterogeneity, and cancer immunology. It also includes improved MultiCellDS outputs, new Matlab routines for reading and processing saved data, and bugfixes. See the README for a full list of changes.
This is the version we used for our resubmission to PLoS Computational Biology. Preprint available at: https://doi.org/10.1101/088773.

July 30, 2017: We released PhysiCell 1.2.0, which contains a reworked Phenotype that should be much easier to use. Motility is now extensively improved, allowing implementation of both We include an all new user manual on all the main functions and classes; see the documentation folder in your download. Lastly, this is the first version to include a Virtual Machine appliance version: if you have a virtual machine like VirtualBox installed, you can import the PhysiCell virtual machine to get a complete graphical Linux OS, compiler, and latest version of PhysiCell. See the README for a full list of changes.

May 17, 2017: We released PhysiCell 1.1.0, which contains numerous simplifications for creating new projects, fast SVG (scalable vector graphics) cross-sections (as virtual pathology), and preliminary MultiCellDS outputs. See the README for a full list of changes.

September 27, 2016: We submitted PhysiCell to PLoS Computational Biology as a software article. As part of that submission, PhysiCell is now available as open source, under the BSD license.

Method, accuracy, and performance Back to top

PhysiCell extends the agent-based model from Macklin et al. (2012) to 3D, with improved sub-models for cell volume regulation, cell cycling, apoptosis, and necrosis. It uses cross-platform compatible C++ (tested on OSX, Linux, and Windows), and it has been parallelized using OpenMP. More details will be available once the method is fully published.

Computational cost scales linearly with the number of simulated cells, and we have tested all the major software components for numerical accuracy and convergence. Simulations up to 1 million cells are feasible on a modern Intel i7 processor with 16-32 GB of system memory. Larger simulations are feasible on HPC compute nodes.

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We'll post some updated examples once PhysiCell is published. In the meantime, please enjoy this early simulation test of a 3-D hanging-drop tumor spheroid.

Licensing and disclaimers Back to top

PhysiCell is licensed under the (3-Clause) BSD License. It is GPL v2 and v3 compatible, and suitable for commercial use in many circumstances.

PhysiCell is an academic/scientific code, and it should not be used as the basis for individual medical decisions. (That's what peer review, clinical trials, and FDA oversight are for!) Always consult your physician when making medical decisions.

Downloads Back to top

Software

PhysiCell is available for download at SourceForge. Each download includes a tutorial and code examples.

Most recent versions

Version Release Date Download link
1.2.1 1 September 2017 http://bit.ly/2wAc4PX [sf.net] (zipped source)
http://bit.ly/2wCC3ol [sf.net] (virtual appliance)
Notes: New code samples for multicellular bioengineering, cancer heterogeneity, cancer immunology. Bugfixes. Improved MultiCellDS output.
1.2.0 30 July 2017 http://bit.ly/2pTwgup [sf.net] (zipped source)
http://bit.ly/2vY51P1 [sf.net] (virtual appliance)
Notes: Major Phenotype rewrite, usability improvements, new motility, full user guide.
1.1.1 18 May 2017 http://bit.ly/2pTwgup [sf.net]
Notes: Minor bugfixes
1.1.0 16 May 2017 http://bit.ly/2pPmERw [sf.net]
Notes: Usability, visualization, and MultiCellDS improvements
1.0.0 12 September 2016 http://bit.ly/2cqoAob [sf.net]
Notes: First public release

Documentation

PhysiCell Method Paper:
Ghaffarizadeh et al. (2017, in revision) published the original version of PhysiCell. It is under review and revision at PLoS Computational Biology.
bioRxiv preprint: https://doi.org/10.1101/088773
PhysiCell Method Paper: Supplementary Materials
The supplementary materials to Ghaffarizadeh et al. (2017, in revision) includes more information on the underlying algorithms, reference parameter values, and extensive testing results.
User Manual
A full user manual is included with every PhysiCell download.
Tutorials and blog posts
We have posted tutorials on setting up a compatible g++ development, common compiling problems, and using PhysiCell. Please visit:

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

Support Back to top

For support, please contact Paul Macklin.

If you plan to use PhysiCell in a grant proposal or a project, please consider including Paul Macklin as a Co-I or consultant for more dedicated support.

Tutorials

We are creating numerous tutorials on using PhysiCell. Please visit:

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

New users should particularly note the tutorials on preparing your development environment for C++ programs with OpenMP.

Please note that OSX by default uses "fake" gcc (an alias that substitutes LLVM/Clang, often without OpenMP suppport) in their command line. Those users should install a full version gcc if they can't compile PhysiCell. See this tutorial.

Bugs and Support Requests

Users can submit bug reports and support requests at:

https://sourceforge.net/projects/physicell/support?source=navbar

Development Roadmap Back to top

More soon.

How to Cite PhysiCell Back to top

PhysiCell is under review and revision at PLoS Computational Biology. For now, please reference our bioRxiv preprint:

We built our model using PhysiCell (Version 1.2.1). [1]

[1] A. Ghaffarizadeh, S.H. Friedman, S.M. Mumenthaler, and P. Macklin, PhysiCell: an Open Source Physics-Based Cell Simulator for 3-D Multicellular Systems, bioRxiv 088773, 2016. DOI: 10.1101/088773.

We will update this citation information once PhysiCell has been accepted for publication.

You can also cite an earlier (2-D) version of the model by our 2012 paper in the Journal of Theoretical Biology:

P. Macklin, M.E. Edgerton, A.M. Thompson, and V. Cristini. Patient-calibrated agent-based modelling of ductal carcinoma in situ (DCIS): From microscopic measurements to macroscopic predictions of clinical progression. J. Theor. Biol. 301:122-40, 2012. DOI: 10.1016/j.jtbi.2012.02.002.

Some Publications and Projects that cite PhysiCell

Nothing just yet. :-)

Additional topics Back to top

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