Description of parameter space and simulation files We varied 8 selected parameters in all combinations: the maximal conductances of the spike-mediated (gSynS) and of graded transmission (gSynG), and of the IP, ICaS, Ileak, Ih, and IK2 currents, across of 0, 25, 50, 75, 100, 125, 150, and 175 percent of their canonical values, and the leak reversal potential across -70 mV, -65 mV, -60 mV, -55 mV, and -50 mV values, resulting in a parameter space of 10,485,760 simulated model instances (10,321,920 of these are HCO instances because they have at least one synaptic component present, and the rest of them, 163,840, are essentially isolated neuron instances but contain twin neurons without any synaptic interaction). We used the same parameter values in each of the paired model neurons. All simulations were started from the same initial conditions, which were different for each of the two neurons (Doloc-Mihu and Calabrese, 2011). ----------------- How to run simulations ------------------ This file explains how to run simulations on a Linux cluster. To start the simulation process you must first make some arrangements. This file explains how to do these arrangements step by step. The files needed are Linux/Unix and Perl scripts implemented by Dr. Cengiz Gunay (cgunay at emory.edu). Click here to download the simulation scripts. Short description --------------------- We give the parameters of the model outside the model in an ASCII input file, in a very convenient format (4 formats accepted at this time). Using the simulation scripts, this input file is transformed into another file (db file) containing all the possible parameter combinations, with each combination on one line. Further, each line will furnish input parameters for each simulation. To run your simulations, you need to have this db file created within the directory where your model is. Steps for running simulations ----------------------------------- (1) Prepare an ASCII file param_ASCII_file.txt (here, called paramLists.txt) that contains your input data. Format for this file: - each line has one parameter and all its values that will be used included between [] and separated by spaces, - the last line is standard: "trial 1 ++" - make sure your file is clean, ie. it doesn't have extra white characters that could appear if the file was created under Window environment. - choose your format according to the type of brute-force approach you will be using. Options are: 1. Additive increments param_name range_low range_high num_steps 2. Multiplicative increments param_name base_val *mul_factor ^num_steps 3. Choose from a list param_name [ val1 val2 ... ] 4. Independent counter (indicates trial number) param_name start_val ++ [increment] E.g, for LEECH the paramLists.txt looks like this (option 3, in the above list): eLeak [ -0.065 -0.055 -0.050 -0.040 -0.030 ] gBar1 [ 0 -0.3 -0.6 0.2 0.4 ] gBar2 [ 0 -0.3 -0.6 0.2 0.4 ] gBar3 [ 0 -0.3 -0.6 0.2 0.4 ] gBar4 [ 0 -0.3 -0.6 0.2 0.4 ] gBar5 [ 0 -0.3 -0.6 0.2 0.4 ] gBar6 [ 0 -0.3 -0.6 0.2 0.4 ] gBar7 [ 0 -0.3 -0.6 0.2 0.4 ] trial 1 ++ (2) Obtain the parameter file containing all combinations of the parameters from the input file (from 1, above). For this, use command: >./paramScanSingle.pl name_param_file < param_ASCII_file.txt E.g.: >./paramScanSingle.pl all_sim_comb < paramLists.txt will create all_sim_comb.par file which contains on each line a combination of the (model) parameters. Note: The Perl script file paramScanSingle.pl reads the param_ASCII_file.txt and creates the parameter combinations file all_sim_comb.par. The first line of this file contains the number of combinations (or, no. of lines in the file, equivalent to the no. of simulations) and the (no. of parameters + 1). The rest of the lines are all the same: "list of parameters no_of_line 0". E.g.(first 5 lines of the all_sim_comb.par file): 390625 9 -0.065 0 0 0 0 0 0 0 1 0 -0.055 0 0 0 0 0 0 0 2 0 -0.050 0 0 0 0 0 0 0 3 0 -0.040 0 0 0 0 0 0 0 4 0 -0.030 0 0 0 0 0 0 0 5 0 Note: you can find the usage of the perl script by typing: >./paramScanSingle.pl (3) Create a db that is a hashtable for the simulations: >./create_perlhash_param_db all_sim_comb.par The output of the command is all_sim_comb.par.db (*.par.db) file which is a db containing a hashtable. This db provides fast access to a simulation based on its hash key from the hashtable (reading its corresponding line from the parameter file is a much slower way of accessing it). Note: The db file is a very large file. So, before creating it, one needs to make sure there is enough space on the disk. Note: You can access data from the database by using dosimnum script: >./dosimnum //gives the usage of the command For accessing line 8 (the 8th combination of parameters) of the all_sim_comb.par.db db: >./dosimnum param_file line_no //general syntax E.g.: >./dosimnum all_sim_comb.par 8 (4) Submit jobs to cluster nodes (make sure you have sge_submit, sge_perlhash.sh, param_ASCII_file.txt, and db_file files created as above in the simulation directory): > ./sge_submit //gives general info on how to run the script E.g., run in the script directory: >./sge_submit mainSimScript.g all_sim_comb.par [options-to-qsub] The sge_submit: - creates the db from the param_file - submits to a specific cluster node a specific simulation (according to its line number); For this, it calls sge_perlhash.sh script with your_genesis_script_to_run and param_file. The sge_perlhash.sh: - sources your bash - set up the current directory for the simulation - sets up a Genesis environment variable to a specific row no. - finally, runs simulation by passing this variable as param to your_genesis_script (here, mainSimScript.g) Alternatively, you can submit certain jobs directly to the cluster: E.g., to submit 3 jobs, numbered 4,5,6: > qsub -t 4:6 ./sge_perlhash.sh mainSimScript.g all_sim_comb.par Last updated June 22, 2012. Please send comments to adolocm@emory.edu.