Example_Spheroid_TNF

Example: spheroid growth under TNF injection

Step-by-step example of running a simulation with PhysiBoSS: growth of a spheroid under TNF injection

In this example, we showed all the steps required to simulate the growth of a spheroid under TNF injection, with the necessary files provided so that it can be reproduced by the user. The parameter file provided is commented to explain the main parameters used in this simulation. The initial file configuration was created with the PhysiBoSS_CreateInitTxtFile executable.

Preparation

Run the simulation

Visualize the results

Preparation

First the simulation folder must be prepared. We used a precise organization of the simulation to be able to automatize the creation, running and analyse of numerous simulations. The main folder (called in this example example_spheroid_TNF) contains:

• the BN folder that contains the boolean network configuration files, which must be named bn_conf.cfg and bn_nodes.bnd. More explanation of those network files, and other networks files for other biological questions (cell cyle, drosophilia patterning, EGF-TNF signalling...) are available on MaBoSS website . In this example, we used the adaptated version of the Cell Fate network presented in PhysiBoSS publication.
• the runs folders: each run folder contain an individual simulation. This is especially usefull to simulate a similar condition, with only one parameter changing in each run folder, or all the same to repeat it for robutness. In this example, we just did one run (run0 folder).
  A run folder must contain the parameter XML file. It can also contains the initial configuration file, as in this example init.txt. The two output subfolders output and microutput that will be used by PhysiBoSS to write the results files must be present.

Below is the image of the folder organization for this example provided with this distribution:

Run the simulation

To run the simulation, open a Terminal window in the (here run0) folder of the simulation and call PhysiBoSS executable:

path_to_PhysiBoSS/bin/PhysiBoSS -p parameters.xml

During the simulations, summary informations are printed to the terminal (initialisation, number of cells dividing, dying, time spent...). It can be more convenient to redirect it to an other file to supress any output when running multiple simulations at once:

path_to_PhysiBoSS/bin/PhysiBoSS -p parameters.xml > msg.txt

Output files are written in the two output folders, and svg snaphots can be written at given frequency to directly visualize the simulation evolution.

This simulation took around 30 min to run on our cluster.

Visualize the results

To visualize 3D+t results of the simulations, we used the software Paraview which allows for high flexibility and intereactive viewing options. In the files available for this example, the state file example_spheroid_TNF.pvsm contains the setting-up of paraview to draw the output files in 3D view. To use it, open Paraview, click on ( File -> Load State...) and select the state file example_spheroid_TNF.pvsm. Then a window to choose the files to visualize will pop up, select in the output folder of the simulation the cells files stack. See the image below for an example of how using Paraview look with our state file proposed on this example: