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 R...

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Detalles Bibliográficos
Autores principales: Noronha, Alberto, Daníelsdóttir, Anna Dröfn, Gawron, Piotr, Jóhannsson, Freyr, Jónsdóttir, Soffía, Jarlsson, Sindri, Gunnarsson, Jón Pétur, Brynjólfsson, Sigurður, Schneider, Reinhard, Thiele, Ines, Fleming, Ronan M T
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408809/
https://www.ncbi.nlm.nih.gov/pubmed/27993782
http://dx.doi.org/10.1093/bioinformatics/btw667
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author Noronha, Alberto
Daníelsdóttir, Anna Dröfn
Gawron, Piotr
Jóhannsson, Freyr
Jónsdóttir, Soffía
Jarlsson, Sindri
Gunnarsson, Jón Pétur
Brynjólfsson, Sigurður
Schneider, Reinhard
Thiele, Ines
Fleming, Ronan M T
author_facet Noronha, Alberto
Daníelsdóttir, Anna Dröfn
Gawron, Piotr
Jóhannsson, Freyr
Jónsdóttir, Soffía
Jarlsson, Sindri
Gunnarsson, Jón Pétur
Brynjólfsson, Sigurður
Schneider, Reinhard
Thiele, Ines
Fleming, Ronan M T
author_sort Noronha, Alberto
collection PubMed
description 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.
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spelling pubmed-54088092017-05-03 ReconMap: an interactive visualization of human metabolism Noronha, Alberto Daníelsdóttir, Anna Dröfn Gawron, Piotr Jóhannsson, Freyr Jónsdóttir, Soffía Jarlsson, Sindri Gunnarsson, Jón Pétur Brynjólfsson, Sigurður Schneider, Reinhard Thiele, Ines Fleming, Ronan M T Bioinformatics Applications Notes 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. Oxford University Press 2017-02-15 2016-11-21 /pmc/articles/PMC5408809/ /pubmed/27993782 http://dx.doi.org/10.1093/bioinformatics/btw667 Text en © The Author 2016. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Noronha, Alberto
Daníelsdóttir, Anna Dröfn
Gawron, Piotr
Jóhannsson, Freyr
Jónsdóttir, Soffía
Jarlsson, Sindri
Gunnarsson, Jón Pétur
Brynjólfsson, Sigurður
Schneider, Reinhard
Thiele, Ines
Fleming, Ronan M T
ReconMap: an interactive visualization of human metabolism
title ReconMap: an interactive visualization of human metabolism
title_full ReconMap: an interactive visualization of human metabolism
title_fullStr ReconMap: an interactive visualization of human metabolism
title_full_unstemmed ReconMap: an interactive visualization of human metabolism
title_short ReconMap: an interactive visualization of human metabolism
title_sort reconmap: an interactive visualization of human metabolism
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408809/
https://www.ncbi.nlm.nih.gov/pubmed/27993782
http://dx.doi.org/10.1093/bioinformatics/btw667
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