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Database Constraints Applied to Metabolic Pathway Reconstruction Tools
Joint Authors
Mateo, Jordi
Vilaplana, Jordi
Solsona, Francesc
Teixido, Ivan
Usié, Anabel
Karathia, Hiren
Alves, Rui
Source
Issue
Vol. 2014, Issue 2014 (31 Dec. 2014), pp.1-12, 12 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2014-08-17
Country of Publication
Egypt
No. of Pages
12
Main Subjects
Medicine
Information Technology and Computer Science
Abstract EN
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.
American Psychological Association (APA)
Vilaplana, Jordi& Solsona, Francesc& Teixido, Ivan& Usié, Anabel& Karathia, Hiren& Alves, Rui…[et al.]. 2014. Database Constraints Applied to Metabolic Pathway Reconstruction Tools. The Scientific World Journal،Vol. 2014, no. 2014, pp.1-12.
https://search.emarefa.net/detail/BIM-1051790
Modern Language Association (MLA)
Vilaplana, Jordi…[et al.]. Database Constraints Applied to Metabolic Pathway Reconstruction Tools. The Scientific World Journal No. 2014 (2014), pp.1-12.
https://search.emarefa.net/detail/BIM-1051790
American Medical Association (AMA)
Vilaplana, Jordi& Solsona, Francesc& Teixido, Ivan& Usié, Anabel& Karathia, Hiren& Alves, Rui…[et al.]. Database Constraints Applied to Metabolic Pathway Reconstruction Tools. The Scientific World Journal. 2014. Vol. 2014, no. 2014, pp.1-12.
https://search.emarefa.net/detail/BIM-1051790
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1051790