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Published on: December 7, 2021
Visual setup of logical models of signaling and regulatory networks with ProMoT
Julio Saez-Rodriguez1, Sebastian Mirschel, Rebecca Hemenway
1Max-Planck-Institute for Dynamics of Complex Technical Systems, Sandtorstr, 1, 39106 Magdeburg, Germany. saezr@mpi-magdeburg.mpg.de <saezr@mpi-magdeburg.mpg.de>
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/.
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