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
- Setting up a 64-bit gcc environment in Windows.
- Setting up gcc / OpenMP on OSX (MacPorts edition)
Note: We highly recommend using Homebrew instead. (See below).
- Setting up gcc / OpenMP on OSX (Homebrew edition)
Note: This is the preferred method for Mac OSX.
- 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
- Frequently Asked Questions (FAQs) for Building PhysiCell
- Your first PhysiCell simulation (coming soon!)
- Building and running the standard PhysiCell sample projects
- Loading and viewing PhysiCell digital snapshots in Matlab
- User-defined model parameters in PhysiCell XML configuration files
- Setting up the microenvironment with the XML configuration file
- PhysiCell-povwriter (for 3-D raytacing renders of your PhysiCell simulations)
- Python-loader (load PhysiCell simulation outputs into Python)