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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

Open Access
Online
ISSN
1613-4516
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Volume 8, Issue 2

Issues

The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks

Neil Swainston
  • Corresponding author
  • Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, M1 7DN, United Kingdom of Great Britain and Northern Ireland
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Kieran Smallbone
  • Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, M1 7DN, United Kingdom of Great Britain and Northern Ireland
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Pedro Mendes
  • Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, M1 7DN, United Kingdom United States of America
  • Virginia Bioinformatics Institute, Virginia Tech, Washington St. 0477, Blacksburg, VA 24061, United States of America
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Douglas B. Kell
  • Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, M1 7DN, United Kingdom of Great Britain and Northern Ireland
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Norman W. Paton
  • Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, M1 7DN, United Kingdom of Great Britain and Northern Ireland
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2011-186

Summary

The generation and use of metabolic network reconstructions has increased over recent years. The development of such reconstructions has typically involved a time-consuming, manual process. Recent work has shown that steps undertaken in reconstructing such metabolic networks are amenable to automation.

The SuBliMinaL Toolbox (http://www.mcisb.org/subliminal/) facilitates the reconstruction process by providing a number of independent modules to perform common tasks, such as generating draft reconstructions, determining metabolite protonation state, mass and charge balancing reactions, suggesting intracellular compartmentalisation, adding transport reactions and a biomass function, and formatting the reconstruction to be used in third-party analysis packages. The individual modules manipulate reconstructions encoded in Systems Biology Markup Language (SBML), and can be chained to generate a reconstruction pipeline, or used individually during a manual curation process.

This work describes the individual modules themselves, and a study in which the modules were used to develop a metabolic reconstruction of Saccharomyces cerevisiae from the existing data resources KEGG and MetaCyc. The automatically generated reconstruction is analysed for blocked reactions, and suggestions for future improvements to the toolbox are discussed.

About the article

Published Online: 2016-10-18

Published in Print: 2011-06-01


Citation Information: Journal of Integrative Bioinformatics, Volume 8, Issue 2, Pages 187–203, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2011-186.

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© 2011 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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