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      MonaLisa--visualization and analysis of functional modules in biochemical networks.

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          Abstract

          Structural modeling of biochemical networks enables qualitative as well as quantitative analysis of those networks. Automated network decomposition into functional modules is a crucial point in network analysis. Although there exist approaches for the analysis of networks, there is no open source tool available that combines editing, visualization and the computation of steady-state functional modules. We introduce a new tool called MonaLisa, which combines computation and visualization of functional modules as well as an editor for biochemical Petri nets. The analysis techniques allow for network decomposition into functional modules, for example t-invariants (elementary modes), maximal common transition sets, minimal cut sets and t-clusters. The graphical user interface provides various functionalities to construct and modify networks as well as to visualize the results of the analysis.

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          Author and article information

          Journal
          Bioinformatics
          Bioinformatics (Oxford, England)
          Oxford University Press (OUP)
          1367-4811
          1367-4803
          Jun 01 2013
          : 29
          : 11
          Affiliations
          [1 ] Molecular Bioinformatics Group, Institute of Computer Science, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt 'Macromolecular Complexes', Robert-Mayer-Strasse 11-15, Frankfurt am Main, Germany.
          Article
          btt165
          10.1093/bioinformatics/btt165
          23564846
          1b189449-f385-4e76-964d-81cf819804c5
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