MonaLisa Project website at Sourceforge

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

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MonaLisa is a Petri net based tool for the analysis of biochemical networks. It comprises an editor supported by an intuitive visualization and animation, and various analysis techniques, focusing on network decomposition, knockout analysis, and other. It includes the computation of elementary modes (T-invariants), P-invariants, Maximal common transition sets (MCT-sets), T-clusters, minimal cut sets (MCS), degree distribution, cluster coefficient distribution.

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.

highlighting of an elementary modein MonaLisa
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.

Download & License

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 dependends 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 downloaded at our Sourceforge download site.


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


To use MonaLisa you have to install Java 6 or higher. To install MonaLisa you have to extract the archive in an arbitrary folder. The archive contains a folder lib with all libraries. This folder must be located in the same folder as MonaLisa.jar. To start MonaLisa just perform a double click on the MonaLisa.jar. If jar files not linked to Java, you need to execute MonaLisa out of your console using the following command:

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.

Code & Development

The source code is included in the src-directory of your MonaLisa release.

The latest version of the MonaLisa code is managed in our non-public subversion repository. If you are interested in the development of MonaLisa, please contact the authors.


You can use the tickets system or the discussion forums at our Sourceforge website to ask questions, report bugs and security issues, request features and other.

Contact & Citing MonaLisa

MonaLisa was written mainly by Jens Einloft at the Molecular Bioinformatics group of Ina Koch at Johann Wolfgang Goethe-University Frankfurt am Main, Germany.

Contact information

How to cite MonaLisa.

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