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.


CONCLUSIONS
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/.
Saez-Rodriguez
Julio
J
Max-Planck-Institute for Dynamics of Complex Technical Systems, Sandtorstr, 1, 39106 Magdeburg, Germany. saezr@mpi-magdeburg.mpg.de <saezr@mpi-magdeburg.mpg.de>
Mirschel
Sebastian
S
Hemenway
Rebecca
R
Klamt
Steffen
S
Gilles
Ernst Dieter
ED
Ginkel
Martin
M
D000818:Animals; D001671:Biochemistry / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D006801:Humans; D020407:Internet; D008213:Lymphocyte Activation; D008954:Models, Biological; D008962:Models, Theoretical; D011381:Programming Languages; D015398:Signal Transduction; D012984:Software; D049490:Systems Biology; D014584:User-Computer Interface