Version: 2.0
Release date: XXX 2020
Code release doi: XXX
PhysiBoSS 2.0 is a redesign and reimplementation of PhysiBoSS (doi:10.1093/bioinformatics/bty766). It has been conceived as an add-on that expands the PhysiCell (doi:10.1371/journal.pcbi.1005991) agent-based functionalities with intracellular cell signalling using MaBoSS having a decoupled, maintainable and model-agnostic design. PhysiBoSS 2.0 reproduces simulations reported in the original PhysiBoSS publications and can be used with other Boolean models, for instance to predict drug synergy in a gastric adenocarcinoma cell line.
Reference paper: XXX
Reference paper doi: XXX
git clone https://github.com/bsc-life/PhysiBoSSv2.git
cd PhysiBoSSv2
make spheroid-TNF-v2
make
./spheroid-TNF-v2
Key makefile rules, from PhysiCell repository:
make [project-name]: populates the indicated sample project. Use "make" to compile it.
PhysiBoSS [project-name] choices:
- drug-AGS
- spheroid-TNF-v2
- template_BM
PhysiCell [project-name] choices:
- biorobots-sample
- cancer-biorobots-sample
- cancer-immune-sample
- heterogeneity-sample
- template
- template2D
- template3D
- virus-macrophage-sample
make : compiles the current project. If no project has been defined, it first populates the cancer heterogeneity 2D sample project and compiles it
make list-projects : list all available sample projects
make clean : removes all .o files and the executable, so that the next "make" recompiles the entire project
make data-cleanup : clears out all simulation data
make reset : de-populates the sample project and returns to the original PhysiCell state. Use this when switching to a new PhysiCell sample project.
Visit http://MathCancer.org/blog for tutorials and help on PhysiCell.