BoolNetR2GINsim

The aim of this project is to provide a collection of scripts to generate random Boolean logical models using BoolNetR.

For the moment, the only script available generates models compatible to the GINsim modeling and simulation tool in the GINML format, without any graphical (node positioning) information.

Requirements?

You should have R statistical software environment installed (http://www.r-project.org) together with the BoolNetR package (http://cran.r-project.org/web/packages/BoolNet/index.html).

How to use it?

You can run it using the following command line format:

sh BoolNet2GINsimGINML.sh <filename> <nGenes> <reg-type:same|poisson> <arg> <param-type:random|and|or>

where the arguments have the following semantics:

• filename - is the name of the file to be written without extension
• nGenes - is the number of nodes in the network
• reg-type - the type of regulator selection:
• same - all genes will have the same # regulators
• poisson - the # regulators of each gene will follow a poisson distribution
• arg - if (type=same) arg <- #reg else arg <- lambdaParam
• param-type - the type of parameter selection per node
• random - randomly selected following an uniform distribution
• and - parameters are selected to perform an AND on regulators
• or - parameters are selected to perform an OR on regulators

Authors

Pedro T. Monteiro