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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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Citation and License

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

Published: 10 November 2012

Abstract

Background

Experimental datasets are becoming larger and increasingly complex, spanning different data domains, thereby expanding the requirements for respective tool support for their analysis. Networks provide a basis for the integration, analysis and visualization of multi-omics experimental datasets.

Results

Here we present VANTED (version 2), a framework for systems biology applications, which comprises a comprehensive set of seven main tasks. These range from network reconstruction, data visualization, integration of various data types, network simulation to data exploration combined with a manifold support of systems biology standards for visualization and data exchange. The offered set of functionalities is instantiated by combining several tasks in order to enable users to view and explore a comprehensive dataset from different perspectives. We describe the system as well as an exemplary workflow.

Conclusions

VANTED is a stand-alone framework which supports scientists during the data analysis and interpretation phase. It is available as a Java open source tool from http://www.vanted.org. webcite

Keywords:
Biological networks; Data visualization; Data integration; Data analysis; -Omics; Model simulation