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VANTED v2: a framework for systems biology applications

Hendrik Rohn1*, Astrid Junker1, Anja Hartmann1, Eva Grafahrend-Belau1, Hendrik Treutler1, Matthias Klapperstück1, Tobias Czauderna1, Christian Klukas1 and Falk Schreiber123

Author Affiliations

1 , Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany

2 Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120 Halle, Germany

3 Clayton School of Information Technology, Monash University, Victoria 3800, Australia

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BMC Systems Biology 2012, 6:139  doi:10.1186/1752-0509-6-139

Published: 10 November 2012

Additional files

Additional file 1:

Supplementary tutorial. ZIP file containing the data for recreating Figures 3 and 4. To guide the user, a PPT file is provided, which lists and describes all necessary steps to be performed in VANTED.

Format: ZIP Size: 5.4MB Download file

Open Data

Additional file 2:

Filled experiment data template.VANTED template filled with metabolite data from Sulpice et al.[53], consisting of 64 metabolites, 37 enzymes and morphological parameters for 50 Arabidopsis thaliana ecotypes of climate class A. The file can be opened using MS Excel and imported into VANTED as an experiment dataset.

Format: XLS Size: 123KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Merged SBGN network. Large-scale metabolic network of plant primary metabolism in SBGN. The network has been created with VANTED based on merging different pathways downloaded from MetaCrop. This file serves as the basis for mapping experiment datasets and can be imported into VANTED as a network.

Format: GML Size: 2.1MB Download file

Open Data

Additional file 4:

Merged SBGN network enriched with experimental data. Enriched metabolic SBGN network after mapping additional file 2 onto additional file 3. Metabolite data of 50 Arabidopsis thaliana ecotypes is mapped to the network and visualized as bar charts inside the nodes. This file can be imported into VANTED as a network.

Format: GML Size: 6.6MB Download file

Open Data

Additional file 5:

Merged SBGN network enriched with experimental data and correlation data. Analysis of enriched metabolic SBGN network by performing a 1:n correlation between the morphological parameter fresh weight (FW) and all enriched network nodes. The correlation coefficient is visualized using a global color-code. This file can be imported into VANTED as a network.

Format: GML Size: 7.7MB Download file

Open Data