ReconMap: an interactive visualization of human metabolism

Motivation: A genome‐scale reconstruction of human metabolism, Recon 2, is available but no interface exists to interactively visualize its content integrated with omics data and simulation results. Results: We manually drew a comprehensive map, ReconMap 2.0, that is consistent with the content of Recon 2. We present it within a web interface that allows content query, visualization of custom datasets and submission of feedback to manual curators. Availability and Implementation: ReconMap can be accessed via http://vmh.uni.lu, with network export in a Systems Biology Graphical Notation compliant format released under a Creative Commons Attribution‐NonCommercial‐NoDerivatives 4.0 International License. A Constraint‐Based Reconstruction and Analysis (COBRA) Toolbox extension to interact with ReconMap is available via https://github.com/opencobra/cobratoolbox. Contact: ronan.mt.fleming@gmail.com

[1]  Ines Thiele,et al.  Computational Modeling of Human Metabolism and Its Application to Systems Biomedicine. , 2016, Methods in molecular biology.

[2]  George Papadatos,et al.  The ChEMBL bioactivity database: an update , 2013, Nucleic Acids Res..

[3]  N. Kikuchi,et al.  CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks , 2008, Proceedings of the IEEE.

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

[5]  B. Palsson.  Systems Biology: Properties of Reconstructed Networks , 2006 .

[6]  Jason A. Papin,et al.  MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data , 2014, Bioinform..

[7]  Samik Ghosh,et al.  Integrating Pathways of Parkinson's Disease in a Molecular Interaction Map , 2013, Molecular Neurobiology.

[8]  Ronan M. T. Fleming,et al.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.

[9]  Ronan M. T. Fleming,et al.  Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks , 2016, PLoS Comput. Biol..

[10]  Ronan M. T. Fleming,et al.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.

[11]  Piotr Gawron,et al.  MINERVA—a platform for visualization and curation of molecular interaction networks , 2016, npj Systems Biology and Applications.