Journal Article

MonaLisa—visualization and analysis of functional modules in biochemical networks

Jens Einloft, Jörg Ackermann, Joachim Nöthen and Ina Koch

in Bioinformatics

Volume 29, issue 11, pages 1469-1470
Published in print June 2013 | ISSN: 1367-4803
Published online April 2013 | e-ISSN: 1460-2059 | DOI:
MonaLisa—visualization and analysis of functional modules in biochemical networks

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Summary: 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.

Availability and implementation: MonaLisa is licensed under the Artistic License 2.0. It is freely available at MonaLisa requires at least Java 6 and runs under Linux, Microsoft Windows and Mac OS.


Journal Article.  1008 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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