PhysiCell Tutorials

We have written a series of tutorials for new users to PhysiCell, an open source 3-D (and 2-D) agent-based biological simulation framework for C++ (Ghaffarizadeh et al., 2017, in review).  They are there to walk users through various aspects of PhysiCell, such as setting up g++ and writing a sample project.

Getting ready to use PhysiCell

  1. Setting up a 64-bit gcc environment in Windows.
  2. Setting up gcc / OpenMP on OSX (MacPorts edition)
    Note: We highly recommend using Homebrew instead. (See below).
  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
  5. Frequently Asked Questions (FAQs) for Building PhysiCell

Using PhysiCell

  1. Your first PhysiCell simulation (coming soon!)
  2. Building and running the standard PhysiCell sample projects
  3. Loading and viewing PhysiCell digital snapshots in Matlab
  4. User-defined model parameters in PhysiCell XML configuration files
  5. Setting up the microenvironment with the XML configuration file

PhysiCell Tools

  1. PhysiCell-povwriter (for 3-D raytacing renders of your PhysiCell simulations)
  2. Python-loader (load PhysiCell simulation outputs into Python)