Version: 2.2.3
Release date: 16 September 2024
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
A tutorial, explaining the new functionalities of PhysiBoSS, including the automated input/output mapping, and more, is available as a preprint. Check it out !
Tutorial paper: https://arxiv.org/abs/2406.18371
Tutorial project folder: here
git clone https://github.com/PhysiBoSS/PhysiBoSS.git
cd PhysiBoSS
make physiboss-tnf-model
make
./spheroid_TNF_modelThe 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-sample
- physiboss-tutorial
- physiboss-tutorial-invasion
- physiboss-tnf-model
-
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
- cancer-metabolism-sample
- interaction-sample
- mechano-sample
- rules-sample
- physimess-sample
- custom-division-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.
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.
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.