ReconMap: An interactive visualisation of human metabolism
Alberto Noronha, Anna Dr\"ofn Danielsd\'ottir, Freyr J\'ohannsson,, Soffia J\'onsd\'ottir, Sindri Jarlsson, J\'on P\'etur Gunnarsson,, Sigur{\dh}ur Brynj\'olfsson, Piotr Gawron, Reinhard Schneider, Ines Thiele,, and Ronan M. T. Fleming
TL;DR
ReconMap 2.0 provides an interactive web-based visualization tool for human metabolism reconstructions, integrating omics data and simulation results to facilitate exploration and analysis.
Contribution
It introduces ReconMap 2.0, a comprehensive, interactive visualization platform for human metabolic reconstructions, integrated with a web interface and compatible with existing analysis tools.
Findings
Accessible via web with network export in SBML format
Supports visualization of custom datasets and user feedback
Compatible with COBRA Toolbox for analysis
Abstract
A genome-scale reconstruction of human metabolism, Recon 2, is available but no interface exists to interactively visualise its content integrated with omics data and simulation 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. ReconMap can be accessed via http://vmh.uni.lu, with network export in a Systems Biology Graphical Notation compliant format. A Constraint-Based Reconstruction and Analysis (COBRA) Toolbox extension to interact with ReconMap is available via https://github.com/opencobra/cobratoolbox.
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Taxonomy
TopicsMicrobial Metabolic Engineering and Bioproduction · Bioinformatics and Genomic Networks · Gene Regulatory Network Analysis