Ontology highlight
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
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]