VANTED v2: a framework for systems biology applications

Abstract

BackgroundExperimental 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.ResultsHere 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.ConclusionsVanted 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.

Mathematically modelling the dynamics of cholesterol metabolism and ageing

“…Figure 1 is an adaptation of the previous SBGN diagram generated by Mc Auley et al (2012). The SBGN diagrams were developed with VANTED (Version 2.2.1, http://vanted.ipk-gatersleben.de/, http://www.sbgn.org/Main_Page) (Rohn et al, 2012). To incorporate the additional information into the SBGN diagram, the compartment previously referred to as 'intestine' was divided into 3 sub-compartments, 'intestinal lumen', 'jejunocytes' and 'ileocytes'.…”

A mathematical model of microbial folate biosynthesis and utilisation: implications for antifolate development

“…All reactions are listed in Table S1 and all metabolites and their abbreviations are listed in Table S2. The vectorial assembly of this model was created with systems biology graphical notation (SBGN) (http://www.sbgn.org/Main_Page) 30 and implemented in VANTED (Version 2.2.1, http://vanted.ipk-gatersleben.de/) 31 . We then converted this biochemical network into a series of reactions (Tables 1 and S1) and assembled them in Version 4.14.89 of the modelling and simulation software tool Copasi 32 .…”

Technical Challenges in Mass Spectrometry-Based Metabolomics

“…25,63,64) e visualization environment and interpretation tools such as VANTED (https://immersive-analytics.infotech.monash.edu/vanted/) and metabolite set enrichment analysis via Metaboanalyst Web page (http://www.metaboanalyst.ca/) are also available for metabolome data. [65][66][67] In addition to being an important tool of the biological analysis, metabolomics has the potential of becoming an essential part of the transomics analysis that integrates other omics such as genomics, transcriptomics, and proteomics. [68][69][70] …”