MetReS, an Efficient Database for Genomic Applications
| Autor: | Jordi Vilaplana, Francesc Solsona, Jordi Mateo, Ivan Teixidó, Rui Alves, Marc Pifarré |
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| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Computer science Big data computer.software_genre Genomic databases 03 medical and health sciences Software Databases Genetic Genetics Animals Data Mining Humans Molecular Biology Database Whole Genome Sequencing business.industry InformationSystems_DATABASEMANAGEMENT Genomics Computational Mathematics ComputingMethodologies_PATTERNRECOGNITION 030104 developmental biology Computational Theory and Mathematics Modeling and Simulation business computer |
| Zdroj: | Journal of computational biology : a journal of computational molecular cell biology. 25(2) |
| ISSN: | 1557-8666 |
| Popis: | MetReS (Metabolic Reconstruction Server) is a genomic database that is shared between two software applications that address important biological problems. Biblio-MetReS is a data-mining tool that enables 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 processes of interest and their function. The main goal of this work was to identify the areas where the performance of the MetReS database performance could be improved and to test whether this improvement would scale to larger datasets and more complex types of analysis. The study was started with a relational database, MySQL, which is the current database server used by the applications. We also tested the performance of an alternative data-handling framework, Apache Hadoop. Hadoop is currently used for large-scale data processing. We found that this data handling framework is likely to greatly improve the efficiency of the MetReS applications as the dataset and the processing needs increase by several orders of magnitude, as expected to happen in the near future. |
| Databáze: | OpenAIRE |
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