Files: ShellPrepMultiSim.sh and PrepMultiSim.pm

Create a project folder with the name of .pmbss file, with all data/inputs and a shell script with the name of the .pmbss file. Launching the shell script runs (multiple) MaBoSS and creates the tables (if specified).

source ShellPrepMultiSim.sh File.pmbss

The file File.pmbss contain the following fields:

    MABOSS = Executable_name;
    BND= bnd_file.bnd;
    CFG= cfg_file.cfg;

The file File.pmbss can contain the optional fields:

    INIT_COND=[Previous_model.bnd,Previous_model_probtraj.csv,#line_number]
    MUT= First_node Second_Node ...;
    COMB_MUT=#number_of_possible_combined_mutation;
    VAR_SENS=[$External_variable1,Suffix_to_add] [$External_variable2,Suffix_to_add]  ...;
    COMB_VAR_SENS=#number_of_possible_combined_variable_sensitivity;
    TRAJ_TABLE=yes;
    STAT_TABLE=[yes,#probability_threshold];

Default number of possible combined mutation/variable sensitivity is 1 (if COMB_MUT or COMB_VAR_SENS are not specified).

Avoid space in file names.

PrepMultiSim.pm should be in the working directory or accessible (installed as a perl library or accessible within an environment variable). If it is in the working folder, it is copied in the project folder.
The file File.pmbss can be in another location (eg /dir1/dir2/File.pmbss or ../../dir/File.pmbss).
The inputs files (.bnd, .cfg, Previous_model_probtraj) can be other locations.
MaBoSS executable name should be an executable file or accessible within PATH variable. If MaBoSS executable name is a readable file, it is copied in the project folder.