run.pl

#!/bin/perl
#*****************************************************
# A simple model of a single AZ at the calyx of Held *
#                                                    *                
#                                                    *
#                                                    *
#                                                    *
# Matthias Hennig                                    *
# mhennig@inf.ed.ac.uk                               *
#*****************************************************
#source: https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=85981
#Used by D.Kufel

# This script takes two parameters, the first is the 
# identification number of the simulation ($simid    
# in preparesimulation.py) and the second    
# the random seed for the current simulation          
# ($run in preparesimulation.py)     

print "running simulation: @ARGV[0], @ARGV[1]\n";

system "/bin/rm", "-f", "chkpt_pos";

$simid = @ARGV[0];
$run = @ARGV[1];

# prepare the file that contains the fusion pore dimension
open(PS, ">pore_scale");
print PS "check_time = 5\n";
print PS "abs_time = 5\n";
close(PS);

# adjust this:
$prg = "/home/dominic/bin/mcell"; #here you need to specify the directory of your MCell PATH

# the gradual opening of the fusion pore is approximated by changing the diamater
# every 5\mu s
for ( $chk = 1; $chk <= 61; $chk++) {  

  system $prg, "-seed $run", "calyx_@ARGV[0]\_@ARGV[1].mdl";

  # adist the pore if time < 300\mu s
  if ( $chk < 60 ) {
    open(PS, ">pore_scale");
    print PS "check_time = 5\n";
    $at = $chk*5+5;
    print PS "abs_time = $at\n";
    close(PS);
  } else {       # or run the rest of the simulation with a constant maximal pore diameter
    open(PS, ">pore_scale");
    print PS "check_time = 3000\n";
    print PS "abs_time = 3000\n";
    close(PS);
  }
}