Abstract
BackgroundThe 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.ResultsHerein 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.ConclusionNew 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 .
Highlights
The analysis of biochemical networks using a logical (Boolean) description is an important approach in Systems Biology
New techniques based on a logical formalism – in combination with graph-theoretical methods applied to the underlying interaction graph – have been proposed for the analysis of large-scale signaling and regulatory networks [6]
These methods have been implemented in CellNetAnalyzer (CNA), allowing structural analysis of large networks within a GUI [7]
Summary
The analysis of biochemical networks using a logical (Boolean) description is an important approach in Systems Biology. New methods have been proposed to analyze large signaling and regulatory networks using this formalism. New techniques based on a logical formalism – in combination with graph-theoretical methods applied to the underlying interaction graph – have been proposed for the analysis of large-scale signaling and regulatory networks [6]. These methods have been implemented in CellNetAnalyzer (CNA), allowing structural analysis of large networks within a GUI [7]. The procedure for setting up large-scale networks by hand, of both the graph and text, can be a cum-
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