VANTED V2: a Framework for Systems Biology Applications

Overview

Journal BMC Syst Biol

Publisher Biomed Central

Specialty Biology

Date 2012 Nov 13

PMID 23140568

Citations 87

Authors

Hendrik Rohn

Astrid Junker

Anja Hartmann

Eva Grafahrend-Belau

Hendrik Treutler

Matthias Klapperstuck

Tobias Czauderna

Christian Klukas

Falk Schreiber

Affiliations

Soon will be listed here.

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.

Citing Articles

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From Gene to Whole Cell: Modeling, Visualization, and Analysis.

Sommer B, Jaeger-Honz S Methods Mol Biol. 2024; 2859:65-92.

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Grone N, Gruneisen B, Klein K, de Bono B, Czauderna T, Schreiber F J Integr Bioinform. 2024; 21(3).

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Medeiros E, Valente M, Honorato L, Ferreira M, Mendoza S, Goncalves D mSystems. 2024; 9(6):e0122623.

PMID: 38717186 PMC: 11237502. DOI: 10.1128/msystems.01226-23.

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