Biological software developped in Serrano's laboratory

SmartCell Useful Scripts

In the Useful script webpage, the users will be able to find some useful scripts in order to automatize the creation of the SmartCell model and/or its simulation.

Creation of the model based on an tab-separated document

This script is generating a single voxel SmartCell model based on a tab-separated text file. The text file is composed by one header line and one line per reaction that needs to be simulated.

The list of column of the text file is:

  • Reaction name: the name of the reaction
  • Rate: the reaction rate of the direct reaction
  • Reverse-rate: the reaction rate of the reverse reaction
  • Reactant: the list of reactants separated by a comma
  • Modifier: the list of modifiers separated by a comma
  • Product: the list of products separated by a comma

The script will first ask you for the name of the tab-separated text file and will then generate a model called smartcell_model.xml

Parameter screening

This script will generate several models based on one input model, screening several possible values for a given parameter.
In order for the script to run correctly, the input model needs to have SCREENING_PARAM for the value of the parameter you want to scan.

The script is run with the following syntax: perl screening_parameter.pl /home/input_model.xml low high step where:

  • /home/input_model.xml is the full path to the xml input model
  • low is the starting value for the parameter
  • high is the ending value for the parameter
  • step is the step value for the parameter screening

This will create the different xml files, the output folders, the shell files and submit all jobs to a Sun Grid Engine cluster.