ReMatch

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

E. Pitkänen (Corresponding Author), A. Åkerlund, A. Rantanen, Paula Jouhten, E. Ukkonen

Research output: Contribution to journalArticleScientificpeer-review

13 Citations (Scopus)

Abstract

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/.
Original languageEnglish
Pages (from-to)188-200
Number of pages13
JournalJournal of integrative bioinformatics
Volume5
Issue number2
DOIs
Publication statusPublished - 2008
MoE publication typeA1 Journal article-refereed

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Metabolic Flux Analysis
Carbon
Databases
Metabolic Networks and Pathways
Names
Controlled Vocabulary
Software

Cite this

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title = "ReMatch: A web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis",
abstract = "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/.",
author = "E. Pitk{\"a}nen and A. {\AA}kerlund and A. Rantanen and Paula Jouhten and E. Ukkonen",
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ReMatch : A web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis. / Pitkänen, E. (Corresponding Author); Åkerlund, A.; Rantanen, A.; Jouhten, Paula; Ukkonen, E.

In: Journal of integrative bioinformatics, Vol. 5, No. 2, 2008, p. 188-200.

Research output: Contribution to journalArticleScientificpeer-review

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AU - Ukkonen, E.

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AB - 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/.

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DO - 10.2390/biecoll-jib-2008-102

M3 - Article

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EP - 200

JO - Journal of integrative bioinformatics

JF - Journal of integrative bioinformatics

SN - 1613-4516

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