UPMaBoSS computes the evolution and the dynamics of a population of cells taking into account both their intracellular and intercellular regulations.
Simulations with UPMaBoSS are based on a logical model describing the intracellular regulations (logical regulatory graph complemented with logical rules), taking into account cell death, cell division, and intercellular communications.
The logical model of an individual cell is described as a MaBoSS model. At predefined intervals, the simulation of the cell population is stopped and the status of each cell of the population is updated according to the value of the variables representing cell death and cell division, and the value of the variables accounting for the activation or inhibition of signals coming from other cells. The simulation is then continued with the updated conditions until the maximum simulation time is reached. Since MaBoSS results are probabilistic, the simulation outputs of UpPMaBoSS can be interpreted as the behaviour of a cell population.
To run UPMaBoSS, three files are needed: a model file (in BND format), a configuration file with the transition rates, the simulation parameters and the initial conditions (in CFG format), and a file defining the update parameters (in UPP format).
docker run -p 8888:8888 -d sysbiocurie/upmaboss
Then open a browser at the following url : http://localhost:8888/tree/UPMaBoSS/
git clone https://github.com/sysbio-curie/UPMaBoSS-docker.git
conda create -n umb -c colomoto -c potassco pymaboss ginsim-python notebook seaborn
conda activate umb
jupyter notebook
Then open a browser at the following url : http://localhost:8888/tree/UPMaBoSS-docker/