Day: August 31, 2017

Running the PhysiCell sample projects

Posted in agent-based model, C++, PhysiCell - August 31, 2017 - 0 Comment

Introduction

In PhysiCell 1.2.1 and later, we include four sample projects on cancer heterogeneity, bioengineered multicellular systems, and cancer immunology. This post will walk you through the steps to build and run the examples.

If you are new to PhysiCell, you should first make sure you’re ready to run it. (Please note that this applies in particular for OSX users, as Xcode’s g++ is not compatible out-of-the-box.) Here are tutorials on getting ready to Run PhysiCell:

  1. Setting up a 64-bit gcc environment in Windows.
  2. Setting up gcc / OpenMP on OSX (MacPorts edition)
  3. Setting up gcc / OpenMP on OSX (Homebrew edition)
    Note: This is the preferred method for Mac OSX.
  4. Getting started with a PhysiCell Virtual Appliance (for virtual machines like VirtualBox)
    Note: The “native” setups above are preferred, but the Virtual Appliance is a great “plan B” if you run into trouble

Please note that we expect to expand this tutorial.

Building, running, and viewing the sample projects

All of these projects will create data of the following forms:

  1. Scalable vector graphics (SVG) cross-section plots through z = 0.0 μm at each output time. Filenames will look like snapshot00000000.svg.
  2. Matlab (Level 4) .mat files to store raw BioFVM data. Filenames will look like output00000000_microenvironment0.mat (for the chemical substrates) and output00000000_cells.mat (for basic agent data).
  3. Matlab .mat files to store additional PhysiCell agent data. Filenames will look like output00000000_cells_physicell.mat.
  4. MultiCellDS .xml files that give further metadata and structure for the .mat files. Filenames will look like output00000000.xml.

You can read the combined data in the XML and MAT files with the read_MultiCellDS_xml function, stored in the matlab directory of every PhysiCell download. (Copy the read_MultiCellDS_xml.m and set_MultiCelLDS_constants.m files to the same directory as your data for the greatest simplicity.)

(If you are using Mac OSX and PhysiCell version > 1.2.1, remember to set the PHYSICELL_CPP environment variable to be an OpenMP-capable compiler – rf. Homebrew setup.)

 Biorobots (2D)

Type the following from a terminal window in your root PhysiCell directory:

make biorobots-sample
make 
./biorobots
make reset # optional -- gets a clean slate to try other samples

Because this is a 2-D example, the SVG snapshot files will provide the simplest method of visualizing these outputs. You can use utilities like ImageMagick to convert them into other formats for publications, such as PNG or EPS.

Anti-cancer biorobots (2D)

make cancer-biorobots-sample
make 
./cancer_biorobots
make reset # optional -- gets a clean slate to try other samples

Cancer heterogeneity (2D)

make heterogeneity-sample
make project
./heterogeneity
make reset # optional -- gets a clean slate to try other samples

Cancer immunology (3D)

make cancer-immune-sample
make 
./cancer_immune_3D
make reset # optional -- gets a clean slate to try other samples

 

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