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


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/.

SUBMITTER: Saez-Rodriguez J 

PROVIDER: S-EPMC1665465 | biostudies-literature | 2006 Nov

REPOSITORIES: biostudies-literature

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Publications

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

Saez-Rodriguez Julio J   Mirschel Sebastian S   Hemenway Rebecca R   Klamt Steffen S   Gilles Ernst Dieter ED   Ginkel Martin M  

BMC bioinformatics 20061117


<h4>Background</h4>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.<h4>Results</h4>Herein we present a flexible framework for setting up  ...[more]

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