title: VANTED v2: a framework for systems biology applications.
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.
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany. rohn@ipk-gatersleben.de
authors.forename: Hendrik
authors.initials: H
authors.lastname: Rohn
authors.forename: Astrid
authors.initials: A
authors.lastname: Junker
authors.forename: Anja
authors.initials: A
authors.lastname: Hartmann
authors.forename: Eva
authors.initials: E
authors.lastname: Grafahrend-Belau
authors.forename: Hendrik
authors.initials: H
authors.lastname: Treutler
authors.forename: Matthias
authors.initials: M
authors.lastname: Klapperstück
authors.forename: Tobias
authors.initials: T
authors.lastname: Czauderna
authors.forename: Christian
authors.initials: C
authors.lastname: Klukas
authors.forename: Falk
authors.initials: F
authors.lastname: Schreiber
mesh_terms: D017360:Arabidopsis / Q000166:cytology / Q000201:enzymology / Q000378:metabolism; D003196:Computer Graphics; D012984:Software; D049490:Systems Biology / Q000379:methods*