MetExploreViz: web component for interactive metabolic network visualization

Abstract Summary MetExploreViz is an open source web component that can be easily embedded in any web site. It provides features dedicated to the visualization of metabolic networks and pathways and thus offers a flexible solution to analyse omics data in a biochemical context. Availability and implementation Documentation and link to GIT code repository (GPL 3.0 license) are available at this URL: http://metexplore.toulouse.inra.fr/metexploreViz/doc/

[1]  Susumu Goto,et al.  Data, information, knowledge and principle: back to metabolism in KEGG , 2013, Nucleic Acids Res..

[2]  Bernhard O. Palsson,et al.  Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways , 2015, PLoS Comput. Biol..

[3]  Peter D. Karp,et al.  Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology , 2015, Briefings Bioinform..

[4]  Michael P. Barrett,et al.  MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks , 2010, Nucleic Acids Res..

[5]  Gary D. Bader,et al.  Cytoscape.js: a graph theory library for visualisation and analysis , 2015, Bioinform..

[6]  Leen Stougie,et al.  Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure , 2013, Bioinform..

[7]  Daniel Jacob,et al.  Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics , 2014, Bioinform..

[8]  Mathieu Bastian,et al.  Gephi: An Open Source Software for Exploring and Manipulating Networks , 2009, ICWSM.

[9]  Fabien Jourdan,et al.  Computational methods to identify metabolic sub‐networks based on metabolomic profiles , 2017, Briefings Bioinform..

[10]  Ronan M. T. Fleming,et al.  A community-driven global reconstruction of human metabolism , 2013, Nature Biotechnology.

[11]  Michael L. Creech,et al.  Integration of biological networks and gene expression data using Cytoscape , 2007, Nature Protocols.

[12]  Christoph Steinbeck,et al.  MetaboLights: An Open‐Access Database Repository for Metabolomics Data , 2016, Current protocols in bioinformatics.

[13]  Piotr Gawron,et al.  ReconMap: an interactive visualization of human metabolism , 2016, Bioinform..

[14]  E. Callaway The visualizations transforming biology , 2016, Nature.

[15]  C. Junot,et al.  Direct introduction of biological samples into a LTQ-Orbitrap hybrid mass spectrometer as a tool for fast metabolome analysis. , 2008, Analytical chemistry.

[16]  Peter D. Karp,et al.  Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology , 2016, Briefings Bioinform..