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The MarVis-Suite - Marker Visualization, Filtering and Clustering



The MarVis-Suite (Marker Visualization) is a toolbox for interactive ranking, filtering, clustering, visualization and analysis of intensity-based profile vectors (marker candidates) as obtained e.g. from metabolomic fingerprinting/profiling or gene expression experiments. The clustering algorithm is based on a realization of one-dimensional self-organizing maps (1D-SOMs). Additionally, the MarVis-Suite includes specialized functions for analysis of mass spectrometry data in the context of untargeted Metabolomics studies, such as adduct and isotope correction and molecular formula calculation.

Within the MarVis-Suite framework the MarVis-Filter software provides functions for import of raw data files, ranking and filtering, while the MarVis-Cluster interface was designed for high-level visualization and cluster analysis. High quality filtered data sets from MarVis-Filter can easily be exchanged with MarVis-Cluster. Nonetheless, MarVis-Cluster can also be utilized as independent tool.

MarVis-Cluster Screenshot Thumbnail

click here to view enlarged



The MarVis-Suite software is free for academic use. It comes with no guarantee or warranty at all. Use it at your own risk. Please send questions, bug reports and feature requests to marvis(AT)gobics(DOT)de .




Download section


MarVis-Filter and MarVis-Cluster (2011) [1]


Currently, the MarVis-Suite is available for Microsoft Windows® XP/Vista/7. Click the following link to download the install package and follow the steps in the README-file.

Download MarVis-Suite install package for Windows XP/Vista/7 (240 MB)


The MarVis-Suite documentation can be found here.

Data sets (2011) [1,2]


Download LC/MS raw data matrices (including method description) of the case study for wounding in plants as CSV files (MarkerLynx Marker Report, unpolar extraction phase, negative and positive ionization mode).

The original MarVis(-Cluster) tool (2009) [3]


The original MarVis tool is available for Microsoft Windows® XP/Vista/7 and Linux x86. Click the following links to download the install packages and follow the steps in the README-file. MarVis was originally developed for the Windows operating system and then ported to Linux. Therefore we recommend the Windows version. When installing and testing MarVis on Linux (Ubuntu 8.10, Fedora 10, openSuse 11.0) a number of additional packages had to be installed and minor bugs regarding the GUI-elements occurred. For experienced users we have added the corresponding references to the README-file.

Download MarVis install package for Windows XP/Vista/7 (230 MB)

Download MarVis install package for Linux x86 (290 MB)


The documentation for MarVis can be found here.


References


[1] Kaever A, Landesfeind M, Possienke M, Feussner K, Feussner I, Meinicke P. MarVis-Filter: Ranking, Filtering, Adduct and Isotope Correction of Mass Spectrometry Data. Journal of Biomedicine and Biotechnology 2012, 2012.

[2] Meinicke P, Lingner T, Kaever A, Feussner K, Göbel C, Feussner I, Karlovsky P, Morgenstern B: Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing maps. Algorithms for Molecular Biology 2008, 3:9.

[3] Kaever A, Lingner T, Feussner K, Göbel C, Feussner I, Meinicke P: MarVis: a tool for clustering and visualization of metabolic biomarkers. BMC Bioinformatics 2009, 10:92.