Home
PhysiBoSS (PhysiCell-MaBoSS) is adapted version of PhysiCell (see physicell.mathcancer.org ) to integrate in it boolean network computation inside each cell. PhysiCell is developped in Paul Macklin's lab (mathcancer.org). MaBoSS and PhysiBoSS are developped in the Computational Systems Biology of Cancer group (sysbio.curie.fr)
Code is written in C++ and open-source. In PhysiCell, there are two main part: BioFVM part which handle the diffusion/production of molecules (e.g. oxygen) and the PhysiCell part that handle the cells themselves. A cell can have a "classic" implementation of the cell cycle (adapted from PhysiCell1.0 initial implementation), or a cell cycling mode determined by a boolean network assigned to each individual cell (using MaBoSS). Could be easily adapted to other network or implementation.
3 executables are proposed in the PhysiBoSS release: PhysiBoSS which handles the actual simulation, PhysiBoSS_CreateInitTxtFile which offers the possibility to automatically generate an initial state of the simulation file and PhysiBoSS_Plot which allows the user to create an svg file showing a snapshot of the simulation at a specific time point.
PhysiBoSS should be compatible with most Linux and MacOS systems. For Windows operating system or others non compatible systems, a Docker version will be proposed soon. C++ compiler with OpenMP support is required.
First, install and compile MaBoSS, by going into the MaBoSS directory and type 'make'. Or directly type 'make maboss' in the main PhysiBoSS directory. Then type 'make' in the main directory to compile everything. The executables will be created in the 'bin' directory if all goes well. It requires a recent version of c++, at least c++11. Can be compiled in Debug, Release or Proliling modes, to set in the Makefile file, default is Release mode which is the fastest mode.
Summary of the steps to download and install PhysiBoSS on Linux system:
git clone https://github.com/gletort/PhysiBoSS.git
cd PhysiBoSS
cd MaBoSS
make
cd ..
make
To generate/update code specific documentation, type 'make doc' in the main directory. The documentation is generated with doxygen, it can be configured in the Doxyfile file present in this directory.
It will generate the documentation files in the 'doc/html' folder (initially empty in the repository). You can visualize it in any browser by opening 'doc/html/index.html' file.
An 'output' and 'microutput' directories should be present in the main directory of the simulation from which the executable will be called. Ideal structure would be to have a simulation directory containing the parameter file (e.g. parameter.xml), the initial configuration file (optional, e.g. init.txt) and the outputs folder. Informations files will be created in this directory (report.txt). Information on how the simulation is running (initialisation completed or not, current time, wall time) are printed to the screen, we redirected them to the file msg.txt when running them through automated script. report.txt gives a quick summary of the simulation, with the number of cells that divided or die in between output times. In the folder 'output', txt files named 'cells_' followed by the time value are written during the simulation, containing the current cells states (position/size/cycle state).
