# ---PrepareProjectFile File for preparing MaBoSS, to be executed with the command "MBSS_PrepareProjectFile.sh File.pmbss"
# ---A directory "File" will be created
# ---Go to the directory: "cd File/", then run MaBoSS and construct tables within the dedicated shell script: "./File.sh"
#----Avoid spaces in file names
#
#Executable MaBoSS name
MABOSS = MaBoSS;
#
#cfg file
CFG = example.cfg;
#
#BND file
BND = example.bnd;
#
#Construct an initial condition from a previous simulation, by specifying the line number of a probtraj file to set as the initial condition
#INIT_COND=[example_mut.bnd,example_mut/example_mut_probtraj.csv,40];
#
# Build a cfg file for each single mutation of the specified nodes. 
MUT=Mdm2nuc Mdm2cyt;
#
# Extend the set of cfg files by considering mutation combinations up to the specified value
COMB_MUT=2;
#
# Build the cfg file for each parameter variation, specified by an external variable and a suffix to add to the external variable definition
VAR_SENS=[$u_Mdm2nuc , -.5] [$u_Mdm2cyt,* 0.01] [$d_Mdm2nuc,+ 0.03];
#
#Extend the set of cfg files by considering parameter variation combinations up to the specified value
COMB_VAR_SENS=2;
#
#Compute table of probability trajectories? yes, no or fig (for producing pie and trajectory figures)
TRAJ_TABLE=fig;
#
#Compute table of stationary distribution decomposition? yes (with probability cutoff) or no
#STAT_TABLE=[yes,0.004];