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

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

Signal Transduction Networks

Foundation (DFG) and the German Ministery of Education and Research (BMBF). First and foremost I would like to thank Professor Ernst Dieter Gilles for his excellent supervision. He always found the perfect balance between letting scientific freedom and providing the key idea and motivating remark whenever I got stuck. He is a mirror where any future professor should look at. I am also indebt to Professor Jöerg Stelling, who accepted to review my thesis. I am deeply grateful to all the members of the Systems Biology Group at the Max-Planck