PhysiBoSS 2: a sustainable integration of stochastic Boolean and agent-based modelling frameworks

Version: 2.2.2

Release date: 6 August 2023

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

Reference paper doi: 10.1038/s41540-023-00314-4

How to run a PhysiBoSS sample_project inside PhysiCell:

git clone https://github.com/PhysiBoSS/PhysiBoSS.git
cd PhysiBoSS
make physiboss-tnf-model
make
./spheroid_TNF_model

PhysiBoSS documentation:

The documentation of PhysiBoSS is available in the PhysiBoSS User Guide.

Key makefile rules, from PhysiCell repository:

make: compiles the current project. If no project has been defined, it first populates the cancer heterogeneity 2D sample project and compiles it

make project-name: populates the indicated sample project. Use "make" to compile it.

• PhysiBoSS [project-name] choices:

  • physiboss_cell_lines
  • spheroid-TNF-model
  • drug-AGS (coming soon, curently available in the former repo)

• PhysiCell [project-name] choices:

  • template
  • biorobots-sample
  • cancer-biorobots-sample
  • cancer-immune-sample
  • celltypes3-sample
  • heterogeneity-sample
  • pred-prey-farmer
  • virus-macrophage-sample
  • worm-sample
  • ode-energy-sample
  • physiboss-cell-lines-sample
  • cancer-metabolism-sample
  • interaction-sample
  • mechano-sample
  • rules-sample
  • physimess-sample

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.

make save PROJ=name: save the current project (including the Makefile, main.cpp, and everything in ./config and ./custom_modules/) in ./user_projects/name, where name is your choice for the project. If the project already exists, overwrite it.

make load PROJ=name: load the user project name from ./user_projects/name (including the Makefile, main.cpp, and everything in ./config and ./custom_modules/).

make list-user-projects: list all user projects in ./user_projects/. (Use these names without the trailing / in make load PROJ=name.)

make jpeg : uses ImageMagick to convert the SVG files in the output directory to JPG (with appropriate sizing to make movies). Supply OUTPUT=foldername to select a different folder.

make movie : uses ffmpeg to convert the JPG files in the output directory an mp4 movie. Supply OUTPUT=foldername to select a different folder, or FRAMERATE=framerate to override the frame rate.

Legacy version

PhysiBoSS 1.0, as described in PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling, is accessible at https://github.com/PhysiBoSS/PhysiBoSSv1.

Acknowledgements

This work has received funding from the Horizon 2020 projects INFORE (ID: 825070) and PerMedCoE (ID: 951773) and from the Horizon Europe project CREXDATA (ID: 101092749). This work was funded in part by the French government under the management of Agence Nationale de la Recherche as part of the “Investissements d’avenir” programme, reference ANR-19-P3IA-0001 (PRAIRIE 3IA Institute).

We thank Anne L'Hévéder for the PhysiBoSS logo.