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PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks

Version: 2.0

Release date: XXX 2020

Code release doi: XXX

Overview:

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

How to run a PhysiBoSS sample_project inside PhysiCell:

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.