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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<jats:italic>SQL<\/jats:italic>database,<jats:italic>MySQL.<\/jats:italic>Then, the same database was implemented by a<jats:italic>MapReduce<\/jats:italic>-based database named<jats:italic>HBase.<\/jats:italic>The results indicated that the standard configuration of<jats:italic>MySQL<\/jats:italic>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.<\/jats:p>","DOI":"10.1155\/2014\/967294","type":"journal-article","created":{"date-parts":[[2014,8,17]],"date-time":"2014-08-17T17:09:35Z","timestamp":1408295375000},"page":"1-12","source":"Crossref","is-referenced-by-count":1,"title":["Database Constraints Applied to Metabolic Pathway Reconstruction Tools"],"prefix":"10.1155","volume":"2014","author":[{"given":"Jordi","family":"Vilaplana","sequence":"first","affiliation":[{"name":"Computer Science Department & INSPIRES, University of Lleida, Jaume II 69, 25001 Lleida, Spain"}]},{"given":"Francesc","family":"Solsona","sequence":"additional","affiliation":[{"name":"Computer Science Department & INSPIRES, University of Lleida, Jaume II 69, 25001 Lleida, Spain"}]},{"given":"Ivan","family":"Teixido","sequence":"additional","affiliation":[{"name":"Computer Science Department & INSPIRES, University of Lleida, Jaume II 69, 25001 Lleida, Spain"}]},{"given":"Anabel","family":"Usi\u00e9","sequence":"additional","affiliation":[{"name":"CEBAL, IPBeja Campus, 7800 Beja, Portugal"}]},{"given":"Hiren","family":"Karathia","sequence":"additional","affiliation":[{"name":"Department of Basic Medical Sciences & IRBLleida, Edifici Recerca Biomedica I, Universitat de Lleida, Avenida Rovira Roure 80, 25198 Lleida, Spain"}]},{"given":"Rui","family":"Alves","sequence":"additional","affiliation":[{"name":"Department of Basic Medical Sciences & IRBLleida, Edifici Recerca Biomedica I, Universitat de Lleida, Avenida Rovira Roure 80, 25198 Lleida, Spain"}]},{"given":"Jordi","family":"Mateo","sequence":"additional","affiliation":[{"name":"Computer Science Department & INSPIRES, University of Lleida, Jaume II 69, 25001 Lleida, Spain"}]}],"member":"311","reference":[{"key":"8","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-12-387"},{"key":"9","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0016015"},{"key":"5","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-70"},{"key":"6","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti1142"},{"key":"7","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq973"},{"key":"10","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh411"},{"issue":"40","key":"11","doi-asserted-by":"crossref","first-page":"13421","DOI":"10.1021\/jp907908d","volume":"113","year":"2009","journal-title":"The Journal of Physical Chemistry B"},{"volume":"4, article 184","journal-title":"Molecular Systems Biology","year":"2008","key":"12"},{"key":"3","doi-asserted-by":"publisher","DOI":"10.1002\/9780470940105.ch17"},{"issue":"1, article 312","key":"14","volume":"32","year":"2009","journal-title":"IEEE Data Engineering Bulletin"},{"key":"22","doi-asserted-by":"publisher","DOI":"10.1007\/s12026-008-8056-7"},{"issue":"3","key":"23","first-page":"256","volume":"26","year":"2008","journal-title":"Nature Biotechnology"},{"key":"24","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-294X.2008.03954.x"},{"key":"25","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2008.09.006"},{"issue":"2","key":"26","doi-asserted-by":"crossref","first-page":"98","DOI":"10.2174\/157489308784340694","volume":"3","year":"2008","journal-title":"Current Bioinformatics"}],"container-title":["The Scientific World Journal"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/downloads.hindawi.com\/journals\/tswj\/2014\/967294.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/downloads.hindawi.com\/journals\/tswj\/2014\/967294.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/downloads.hindawi.com\/journals\/tswj\/2014\/967294.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,6,22]],"date-time":"2017-06-22T14:50:27Z","timestamp":1498143027000},"score":1,"resource":{"primary":{"URL":"http:\/\/www.hindawi.com\/journals\/tswj\/2014\/967294\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014]]},"references-count":15,"alternative-id":["967294","967294"],"URL":"https:\/\/doi.org\/10.1155\/2014\/967294","relation":{},"ISSN":["2356-6140","1537-744X"],"issn-type":[{"type":"print","value":"2356-6140"},{"type":"electronic","value":"1537-744X"}],"subject":[],"published":{"date-parts":[[2014]]}}}