Software to accompany our paper submitted to BMC Bioinformatics:

High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow. Jonathan Ozik, Nicholson Collier, Justin M. Wozniak, Charles Macal, Chase Cockrell, Samuel H. Friedman, Ahmadreza Ghaffarizadeh, Randy Heiland, Gary An and Paul Macklin

The primary study of interest is the cancer-immune one. To compile PhysiCell for this model:

$ cd studies/cancer-immune/PhysiCell-src
$ make -f Makefile-immune

# your compiler needs to support OpenMP, so you may need to specify it if the previous fails:
$ make -f Makefile-immune CC=g++-7

Assuming it builds without errors, you can then test that it runs, e.g.:

$ mkdir run
$ cd run
$ ../cancer-immune-EMEWS    # this will provide sample parameters for a run.

To run EMEWS, see the EMEWS-scripts directory for instructions. To perform final analysis, see the analysis-scripts directory.