MonaLisa -- Visualization and analysis of functional modules in biochemical networks

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This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

MonaLisa is licensed under the Artistic License 2.0 and depends on non-free software. This is a free software license which is compatible with the GPL according to the FSF. It is the same license that is used by the Perl programming language.

MonaLisa can be directly downloaded from our GitHub repository.

Quickstart

java -jar /PATH/TO/MONALISA/MonaLisa.jar

For big networks, you have to start MonaLisa with more memory for the Java virtual machine:

java -Xmx{MemorySizeInGigabyte}G -jar /PATH/TO/MONALISA/MonaLisa.jar
java -Xmx{MemorySizeInMegabyte}M -jar /PATH/TO/MONALISA/MonaLisa.jar

Now to start, a new project can be created or an existing Petri net or project can be loaded.

MonaLisa is a Petri net-based tool for modeling of biochemical networks. It comprises an editor supported by an intuitive visualization and animation, and various analysis techniques. The analysis focuses on invariant analysis, topological network analysis, knockout analysis, and other. It includes the computation of transition invariants (elementary modes), place invariants, Manatee invariants, maximal common transition sets (MCT-sets), t-clusters, minimal cut sets (MCS), degree distributions, cluster coefficient distributions, and other.

MonaLisa supports interfaces for different systems biology and graph-theoretic formats: SBML, KGML, PNT, APNN, MetaTool, and PNML.

MonaLisa is written in Java using the JUNG library for the network representation and the Apache Batik library for SVG output.

The figure depicts the graphical user interface (GUI) of MonaLisa. On the left side, the analytical part of MonaLisa is shown. Here, the user can select the approaches, define the settings, export the results and/or the PN in different formats. In the middle, the NetViewer represents the PN model of the carbon metabolism of sucrose breakdown pathway in the potato tuber (Koch et al., 2005). The metabolites (places) are drawn as circles and the reactions (transitions) as rectangles. The gray-filled circles indicate clone markers (logical places), i.e. those with equal names occur only once in the underlying graph. The color highlighting indicates all transitions of a single elementary mode/transition invariant, including the corresponding pre- and post-places. On the right side, the ToolBar with all modeling and visualization settings is depicted. The shown menu controls the highlighting of elementary modes, place invariants, and maximal common transition sets. The elementary modes can be divided into several categories like those which are cyclic or have only an input but no output and vice versa.

A documentation of MonaLisa is available online. For a quickstart guide see below.


Development

The source code is available at our public Github repository.

If you are interested in the development of MonaLisa, please contact the authors.

You can use the issue system at our GitHub repository to ask questions, report bugs and security issues, request features and other.

MonaLisa was written in the Molecular Bioinformatics group of Prof. Dr. Ina Koch at Goethe University Frankfurt, Germany. Many students contributed to the current version (in temporal order): Jens Einloft, Jörg Ackermann, Joachim Nöthen, Pavel Balazki, Lilya Mirzoyan, Daniel Noll, Marcel Gehrmann, Marlena Meyer, Marius Kirchner.

Contact information

How to cite MonaLisa.

Download & License || About || Documentation || Code & Development || Support || Contact & Citing