Perform multiple simulations by automatically generating configuration files and run multiple simulation with MBSS_FormatTable.pl. The working directory directory must contain a bnd file a cfg file; MBSS_FormatTable.pl and MaBoSS should be accessible in a command line. The script uses the version 2 of python. Canonical call of MBSS_MultiSim : MBSS_MultipleSim.py config_file.cfg profile_file.txt (optional)mutation_file.txt Config file : config file used as usual input for MaBoSS. This file can be generated by ginSim from a boolean model. Profile file: blocks of 6 lines, each block representing a simulation. The profile file can also be generated on the fly by launching MultiSim.py without providing the profile file. This file is written as blocks of 6 lines, each block representing a simulation. - First line: name of the simulation. - Second line: inactive inputs, separated by commas. Initial states of inactive inputs are set to 0 for the simulation. - Third line: active inputs, separated by commas. Initial states of active inputs are set to 1 for the simulation. - Fourth line: transition rates that are modified. In the bnd, for each node, two transitions rates are associated: ``\$u\_nodename'' ``\$d\_nodename'', like it is done with GINsim export (note that the transition rates you wish to vary need to be have this format for the script to work). In the profile file, the modifications associated to each transition rate correspond to fields separated by commas. Each of these fields is composed of 3 attributes separated by ":": the first attribute is "u" or "d" for up or down; the second attribute is the name of the node; and the third attribute is the value of the rate. - Fifth line: initial states that are modified. Each of these inital states correspond to fields separated by commas. Each of these fields is composed of two attributes separated by ":": the first attribute is the name of the node; and the second attribute is the probability of the node of being active at the initial state step of the simulation. - Sixth line: external nodes. Indicate the name of the nodes that we wish to set as external separated by commas. For instance: simulation_name inactive_input1,inactive_input2,...,inactive_inputn active_inputs1,active_input2,...,active_inputn u:node1:0.1,d:node1:0.1,u:node2:0.03,u:node4:0.23 node2:0.4,node3:0.9,node1:0,node5:0.4 external_node1,external_node2,...,external_noden Mutation file: u:node1,d:node2,...,u:noden d:node1 d;node1,dnode2 Each line represents a mutation profile. Each mutation is separated by comas. Each mutation is composed of two attributes separated by ":". The first attribute is "u" or "d" for knock in or knock out. the second attribute is the name of the node. Each mutation profile will be simulated with each simulation selected from the profile file (2//). The output files will be placed in the working directory. MBSS_MultipleSim.py creates a folder for each simulation, named with the name of the config file followed by the name of the current simulation from the profil file and optionally the name of the mutation profile if one was used. The newly created folder will contain all the regular outputs from MaBoSS. NOTE FOR CLUSTER USE The script allows launching simulation on a cluster, but uses by default a qsub command. You may need to modify the submission command to adapt to your own cluster system. To do so: - open MBSS_MultiSim.py with a text editor - go to line 230 (232), in quote you can find the content of the bash script used to submit the job to the cluster. - modify the command to adapt to your own system (check the documentation of your own cluster system for more details) - save and quit Optionally, in the MBSS_MultipleSim.py file, from line 120 to 131, you can directly modify the simulation parameters such as number of runs per simulation, time interval, etc. To do so, just change the second parameter of the re.sub functions to the desired value.