{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,6,9]],"date-time":"2024-06-09T00:02:41Z","timestamp":1717891361060},"reference-count":24,"publisher":"World Scientific Pub Co Pte Ltd","issue":"05","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J CIRCUIT SYST COMP"],"published-print":{"date-parts":[[2015,6]]},"abstract":"<jats:p>STRIKE is an algorithm which predicts protein\u2013protein interactions (PPIs) and determines that proteins interact if they contain similar substrings of amino acids. Unlike other methods for PPI prediction, STRIKE is able to achieve reasonable improvement over the existing PPI prediction methods. Although its high accuracy as a PPI prediction method, STRIKE consumes a large execution time and hence it is considered to be a compute-intensive application. In this paper, we develop and implement a parallel STRIKE algorithm for high-performance computing (HPC) systems. Using a large-scale cluster, the execution time of the parallel implementation of this bioinformatics algorithm was reduced from about a week on a serial uniprocessor machine to about 16.5 h on 16 computing nodes, down to about 2 h on 128 parallel nodes. Communication overheads between nodes are thoroughly studied.<\/jats:p>","DOI":"10.1142\/s0218126615500747","type":"journal-article","created":{"date-parts":[[2015,3,30]],"date-time":"2015-03-30T14:14:12Z","timestamp":1427724852000},"page":"1550074","source":"Crossref","is-referenced-by-count":2,"title":["Parallel PPI Prediction Performance Study on HPC Platforms"],"prefix":"10.1142","volume":"24","author":[{"given":"Ali A.","family":"El-Moursy","sequence":"first","affiliation":[{"name":"Electrical and Computer Engineering, University of Sharjah, Sharjah, UAE"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wael S.","family":"Afifi","sequence":"additional","affiliation":[{"name":"Computer and Systems, Electronics Research Institute, Cairo, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fadi N.","family":"Sibai","sequence":"additional","affiliation":[{"name":"Computer Operations Department, Saudi Aramco, Dhahran, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Salwa M.","family":"Nassar","sequence":"additional","affiliation":[{"name":"Computer and Systems, Electronics Research Institute, Cairo, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"219","published-online":{"date-parts":[[2015,4,8]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2001.4920"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.153002"},{"key":"rf3","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bth366"},{"key":"rf4","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti721"},{"key":"rf5","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-7-365"},{"key":"rf7","first-page":"419","volume":"2","author":"Lodhi H.","year":"2002","journal-title":"J. Mach. Learning Res."},{"key":"rf8","doi-asserted-by":"publisher","DOI":"10.2165\/00822942-200504010-00005"},{"key":"rf10","doi-asserted-by":"crossref","unstructured":"C.\u00a0Watkins, Advances in Large Margin Classifiers (MIT Press, Cambridge, Massachusetts, USA, 2000)\u00a0pp. 39\u201350.","DOI":"10.7551\/mitpress\/1113.003.0006"},{"key":"rf11","volume-title":"CUDA by Example: An Introduction to General-Purpose GPU Programming","author":"Sanders J.","year":"2010"},{"key":"rf12","doi-asserted-by":"publisher","DOI":"10.1145\/1364644.1364647"},{"key":"rf13","volume-title":"OpenCL Programming Guide","author":"Munshi A.","year":"2011"},{"key":"rf14","volume-title":"Programming Massively Parallel Processors: A Hands-on Approach","author":"Kirk D. B.","year":"2010"},{"key":"rf15","doi-asserted-by":"publisher","DOI":"10.1016\/j.micpro.2008.06.002"},{"key":"rf16","doi-asserted-by":"publisher","DOI":"10.1109\/MM.2011.108"},{"key":"rf17","volume-title":"IBM System Blue Gene Solution: Blue Gene\/Q System Administration","author":"Lakner G.","year":"2013"},{"key":"rf18","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.263"},{"key":"rf22","first-page":"10","author":"Zaki N.","year":"2009","journal-title":"BMC Bioinform."},{"key":"rf24","volume":"4","author":"Sharma C.","year":"2014","journal-title":"Int. J. Adv. Res. Comput. Sci. Software Eng."},{"key":"rf26","first-page":"4673","volume":"22","author":"Thompson J.","year":"1994","journal-title":"Position-Specific Gap Penalties and Weight Matrix Choice, Nucleic Acids Res."},{"key":"rf28","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511574931"},{"key":"rf33","doi-asserted-by":"publisher","DOI":"10.1109\/TPDS.2007.70813"},{"key":"rf37","doi-asserted-by":"publisher","DOI":"10.1147\/rd.521.0093"},{"key":"rf38","volume-title":"Concurrency and Computation","author":"El-Moursy A.","year":"2010"},{"key":"rf39","doi-asserted-by":"publisher","DOI":"10.1002\/cpe.2959"}],"container-title":["Journal of Circuits, Systems and Computers"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S0218126615500747","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,8]],"date-time":"2024-06-08T03:09:38Z","timestamp":1717816178000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S0218126615500747"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,4,8]]},"references-count":24,"journal-issue":{"issue":"05","published-online":{"date-parts":[[2015,4,8]]},"published-print":{"date-parts":[[2015,6]]}},"alternative-id":["10.1142\/S0218126615500747"],"URL":"https:\/\/doi.org\/10.1142\/s0218126615500747","relation":{},"ISSN":["0218-1266","1793-6454"],"issn-type":[{"value":"0218-1266","type":"print"},{"value":"1793-6454","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,4,8]]}}}