Database constraints applied to metabolic pathway reconstruction tools
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Date
2014
Authors
Vilaplana Mayoral, Jordi
Solsona Tehàs, Francesc
Teixidó Torrelles, Ivan
Usié Chimenos, Anabel
Karathia, Hiren
Alves, Rui
Mateo Fornés, Jordi
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Abstract
Our 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.
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The Scientific World Journal, 2014, vol. 2014, p. 1-12