Database constraints applied to metabolic pathway reconstruction tools

dc.contributor.authorVilaplana Mayoral, Jordi
dc.contributor.authorSolsona Tehàs, Francesc
dc.contributor.authorTeixidó Torrelles, Ivan
dc.contributor.authorUsié Chimenos, Anabel
dc.contributor.authorKarathia, Hiren
dc.contributor.authorAlves, Rui
dc.contributor.authorMateo Fornés, Jordi
dc.date.accessioned2015-06-01T12:08:29Z
dc.date.available2015-06-01T12:08:29Z
dc.date.issued2014
dc.description.abstractOur group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the process(es) of interest and their function. It also enables the sets of proteins involved in the process(es) in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database.We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the communication data link to/from the database system. Different database technologies were analyzed.We started the study with a public relational SQL database, MySQL.Then, the same database was implemented by a MapReduce-based database named HBase. The results indicated that the standard configuration of MySQL gives an acceptable performance for low or medium size databases. Nevertheless, tuning database parameters can greatly improve the performance and lead to very competitive runtimes.ca_ES
dc.description.sponsorshipThis work was supported by the MEyC under Contracts TIN2011-28689-C02-02 and BFU20 10-17704. The authors are members of the research groups 2009-SGR145 and 2009- SGR809, funded by the Generalitat de Catalunya.
dc.identifier.doihttps://doi.org/10.1155/2014/967294
dc.identifier.idgrec021571
dc.identifier.issn2356-6140
dc.identifier.urihttp://hdl.handle.net/10459.1/48279
dc.language.isoengca_ES
dc.publisherHindawi Publishing Corporationca_ES
dc.relationMICINN/PN2008-2011/TIN2011-28689-C02-02
dc.relation.isformatofReproducció del document publicat a https://doi.org/10.1155/2014/967294ca_ES
dc.relation.ispartofThe Scientific World Journal, 2014, vol. 2014, p. 1-12ca_ES
dc.rightscc-by, (c) Vilaplana et al., 2014ca_ES
dc.rights.accessRightsinfo:eu-repo/semantics/openAccessca_ES
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/es/*
dc.titleDatabase constraints applied to metabolic pathway reconstruction toolsca_ES
dc.typearticleca_ES
dc.type.versionpublishedVersionca_ES
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