Visual setup of logical models of signaling and regulatory networks with ProMoT.
| Autor: | Saez-Rodriguez J; Max-Planck-Institute for Dynamics of Complex Technical Systems, Sandtorstr, 1, 39106 Magdeburg, Germany. saezr@mpi-magdeburg.mpg.de |
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| Jazyk: | angličtina |
| Zdroj: | BMC bioinformatics [BMC Bioinformatics] 2006 Nov 17; Vol. 7, pp. 506. Date of Electronic Publication: 2006 Nov 17. |
| DOI: | 10.1186/1471-2105-7-506 |
| Abstrakt: | 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/. |
| Databáze: | MEDLINE |
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