Software

Visual setup of logical models of signaling and regulatory networks with ProMoT

Julio Saez-Rodriguez^* , Sebastian Mirschel^* , Rebecca Hemenway , Steffen Klamt , Ernst Dieter Gilles and Martin Ginkel

Max-Planck-Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106 Magdeburg, Germany

author email corresponding author email* Contributed equally

BMC Bioinformatics 2006, 7:506doi:10.1186/1471-2105-7-506

Published:	17 November 2006

Abstract

Background

The analysis of biochemical networks using a logical (Boolean) description is an important approach in Systems Biology. Recently, new methods have been proposed to analyze large signaling and regulatory networks using this formalism. Even though there is a large number of tools to set up models describing biological networks using a biochemical (kinetic) formalism, however, they do not support logical models.

Results

Herein we present a flexible framework for setting up large logical models in a visual manner with the software tool ProMoT. An easily extendible library, ProMoT's inherent modularity and object-oriented concept as well as adaptive visualization techniques provide a versatile environment. Both the graphical and the textual description of the logical model can be exported to different formats.

Conclusion

New features of ProMoT facilitate an efficient set-up of large Boolean models of biochemical interaction networks. The modeling environment is flexible; it can easily be adapted to specific requirements, and new extensions can be introduced. ProMoT is freely available from http://www.mpi-magdeburg.mpg.de/projects/promot/ webcite.