Jump to ContentJump to Main Navigation
Show Summary Details
More options …

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 2018: 0.90

SCImago Journal Rank (SJR) 2018: 0.315

Open Access
See all formats and pricing
More options …
Volume 5, Issue 2


ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis

Esa Pitkänen / Arto Åkerlund / Ari Rantanen / Paula Jouhten
  • Department of Computer Science, University of Helsinki, Finland Finland
  • VTT Technical Research Centre of Finland, Finland
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Esko Ukkonen
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2008-102


y ReMatch is a web-based, user-friendly tool that constructs stoichiometric network models for metabolic flux analysis, integrating user-developed models into a database collected from several comprehensive metabolic data resources, including KEGG, MetaCyc and CheBI. Particularly, ReMatch augments the metabolic reactions of the model with carbon mappings to facilitate 13C metabolic flux analysis.

The construction of a network model consisting of biochemical reactions is the first step in most metabolic modelling tasks. This model construction can be a tedious task as the required information is usually scattered to many separate databases whose interoperability is suboptimal, due to the heterogeneous naming conventions of metabolites in different databases. Another, particularly severe data integration problem is faced in 13C metabolic flux analysis, where the mappings of carbon atoms from substrates into products in the model are required.

ReMatch has been developed to solve the above data integration problems. First, ReMatch matches the imported user-developed model against the internal ReMatch database while considering a comprehensive metabolite name thesaurus. This, together with wild card support, allows the user to specify the model quickly without having to look the names up manually. Second, ReMatch is able to augment reactions of the model with carbon mappings, obtained either from the internal database or given by the user with an easy-touse tool.

The constructed models can be exported into 13C-FLUX and SBML file formats. Further, a stoichiometric matrix and visualizations of the network model can be generated. The constructed models of metabolic networks can be optionally made available to the other users of ReMatch. Thus, ReMatch provides a common repository for metabolic network models with carbon mappings for the needs of metabolic flux analysis community. ReMatch is freely available for academic use at http://www.cs.helsinki.fi/group/sysfys/software/rematch/.

About the article

Published Online: 2016-10-18

Published in Print: 2008-06-01

Citation Information: Journal of Integrative Bioinformatics, Volume 5, Issue 2, Pages 188–200, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2008-102.

Export Citation

© 2008 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

Citing Articles

Here you can find all Crossref-listed publications in which this article is cited. If you would like to receive automatic email messages as soon as this article is cited in other publications, simply activate the “Citation Alert” on the top of this page.

Evangelos Simeonidis and Nathan D. Price
Journal of Industrial Microbiology & Biotechnology, 2015, Volume 42, Number 3, Page 327
Rajib Saha, Anupam Chowdhury, and Costas D Maranas
Current Opinion in Biotechnology, 2014, Volume 29, Page 39
Nicola Zamboni, Sarah-Maria Fendt, Martin Rühl, and Uwe Sauer
Nature Protocols, 2009, Volume 4, Number 6, Page 878
Esa Pitkänen, Paula Jouhten, and Juho Rousu
BMC Systems Biology, 2009, Volume 3, Number 1

Comments (0)

Please log in or register to comment.
Log in