title: MonaLisa--visualization and analysis of functional modules in biochemical networks.
abstract: CONCLUSIONS
  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.
  
  
  METHODS
  MonaLisa is licensed under the Artistic License 2.0. It is freely available at http://www.bioinformatik.uni-frankfurt.de/software.html. MonaLisa requires at least Java 6 and runs under Linux, Microsoft Windows and Mac OS.
authors.affiliation: 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.
authors.forename: Jens
authors.initials: J
authors.lastname: Einloft
authors.forename: Jörg
authors.initials: J
authors.lastname: Ackermann
authors.forename: Joachim
authors.initials: J
authors.lastname: Nöthen
authors.forename: Ina
authors.initials: I
authors.lastname: Koch
mesh_terms: D001669:Biochemical Phenomena; D003196:Computer Graphics; D012984:Software