{"id":"https://openalex.org/W2076580581","doi":"https://doi.org/10.1186/1471-2105-11-s1-s36","title":"Towards high performance computing for molecular structure prediction using IBM Cell Broadband Engine - an implementation perspective","display_name":"Towards high performance computing for molecular structure prediction using IBM Cell Broadband Engine - an implementation perspective","publication_year":2010,"publication_date":"2010-01-01","ids":{"openalex":"https://openalex.org/W2076580581","doi":"https://doi.org/10.1186/1471-2105-11-s1-s36","mag":"2076580581","pmid":"https://pubmed.ncbi.nlm.nih.gov/20122209"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-s1-s36","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s1-s36","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S1-S36","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S1-S36","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5106084064","display_name":"S. P. T. Krishnan","orcid":null},"institutions":[{"id":"https://openalex.org/I3005327000","display_name":"Institute for Infocomm Research","ror":"https://ror.org/053rfa017","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I3005327000","https://openalex.org/I91275662"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"SPT Krishnan","raw_affiliation_strings":["Institute for Infocomm Research, 1 Fusionopolis Way, #21-01, Connexis South Tower, Singapore 138632. krishnan@i2r.a-star.edu.sg","Institute for Infocomm Research, Connexis (South Tower), Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Infocomm Research, 1 Fusionopolis Way, #21-01, Connexis South Tower, Singapore 138632. krishnan@i2r.a-star.edu.sg","institution_ids":["https://openalex.org/I3005327000"]},{"raw_affiliation_string":"Institute for Infocomm Research, Connexis (South Tower), Singapore","institution_ids":["https://openalex.org/I3005327000"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039564589","display_name":"Sim Sze Liang","orcid":null},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Sim Sze Liang","raw_affiliation_strings":["Department of Electrical and Computer Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117576","[Dept. of Electrical and Computer Engineering, National University of Singapore, Singapore.]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117576","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"[Dept. of Electrical and Computer Engineering, National University of Singapore, Singapore.]","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070594442","display_name":"Bharadwaj Veeravalli","orcid":"https://orcid.org/0000-0001-9000-1813"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Bharadwaj Veeravalli","raw_affiliation_strings":["Department of Electrical and Computer Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117576","[Dept. of Electrical and Computer Engineering, National University of Singapore, Singapore.]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117576","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"[Dept. of Electrical and Computer Engineering, National University of Singapore, Singapore.]","institution_ids":["https://openalex.org/I165932596"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5106084064"],"corresponding_institution_ids":["https://openalex.org/I3005327000"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.3734,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.60154486,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"11","issue":"S1","first_page":"S36","last_page":"S36"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.8902999758720398,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.8902999758720398,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.02070000022649765,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.01590000092983246,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8232470750808716},{"id":"https://openalex.org/keywords/ibm","display_name":"IBM","score":0.7126772403717041},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6624306440353394},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.5985679626464844},{"id":"https://openalex.org/keywords/multi-core-processor","display_name":"Multi-core processor","score":0.5973048806190491},{"id":"https://openalex.org/keywords/data-parallelism","display_name":"Data parallelism","score":0.5614160299301147},{"id":"https://openalex.org/keywords/parallelism","display_name":"Parallelism (grammar)","score":0.5447304248809814},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.4712424874305725},{"id":"https://openalex.org/keywords/embarrassingly-parallel","display_name":"Embarrassingly parallel","score":0.455686092376709},{"id":"https://openalex.org/keywords/massively-parallel","display_name":"Massively parallel","score":0.3802470862865448}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8232470750808716},{"id":"https://openalex.org/C70388272","wikidata":"https://www.wikidata.org/wiki/Q5968558","display_name":"IBM","level":2,"score":0.7126772403717041},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6624306440353394},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.5985679626464844},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.5973048806190491},{"id":"https://openalex.org/C61483411","wikidata":"https://www.wikidata.org/wiki/Q3124522","display_name":"Data parallelism","level":3,"score":0.5614160299301147},{"id":"https://openalex.org/C2781172179","wikidata":"https://www.wikidata.org/wiki/Q853109","display_name":"Parallelism (grammar)","level":2,"score":0.5447304248809814},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.4712424874305725},{"id":"https://openalex.org/C126909462","wikidata":"https://www.wikidata.org/wiki/Q5369501","display_name":"Embarrassingly parallel","level":3,"score":0.455686092376709},{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.3802470862865448},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-11-s1-s36","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s1-s36","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S1-S36","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:20122209","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20122209","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:scholarbank.nus.edu.sg:10635/57690","is_oa":false,"landing_page_url":"http://scholarbank.nus.edu.sg/handle/10635/57690","pdf_url":null,"source":{"id":"https://openalex.org/S7407052290","display_name":"National University of Singapore","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Scopus","raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:851adee8d8f348519917ec04dcf19586","is_oa":true,"landing_page_url":"https://doaj.org/article/851adee8d8f348519917ec04dcf19586","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 11, Iss Suppl 1, p S36 (2010)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3009508","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3009508","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-11-s1-s36","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s1-s36","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S1-S36","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334744","display_name":"Institute for Infocomm Research","ror":"https://ror.org/053rfa017"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2076580581.pdf","grobid_xml":"https://content.openalex.org/works/W2076580581.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W1511408336","https://openalex.org/W1519185585","https://openalex.org/W1571090276","https://openalex.org/W2019430444","https://openalex.org/W2025763720","https://openalex.org/W2091323258","https://openalex.org/W2109297587","https://openalex.org/W2114835471","https://openalex.org/W2123241418","https://openalex.org/W2485383890","https://openalex.org/W2502569966"],"related_works":["https://openalex.org/W2950520577","https://openalex.org/W1554644772","https://openalex.org/W2494130044","https://openalex.org/W2003935582","https://openalex.org/W3209384898","https://openalex.org/W74409296","https://openalex.org/W1991844655","https://openalex.org/W1595834484","https://openalex.org/W3170887803","https://openalex.org/W2468095077"],"abstract_inverted_index":{"BACKGROUND:":[0],"RNA":[1,93,286],"structure":[2,95],"prediction":[3],"problem":[4,14,30,198],"is":[5,15,146,227,233,248],"a":[6,174,215,265,281],"computationally":[7],"complex":[8],"task,":[9],"especially":[10,229],"with":[11],"pseudo-knots.":[12],"The":[13,29,183,222,267],"well-studied":[16],"in":[17,129,160,179,191,196,245],"existing":[18,87],"literature":[19,240],"and":[20,32,117,119,199],"predominantly":[21],"uses":[22],"highly":[23],"coupled":[24],"Dynamic":[25,88],"Programming":[26,89],"(DP)":[27,90],"solutions.":[28],"scale":[31],"complexity":[33],"become":[34],"embarrassingly":[35],"humungous":[36],"to":[37,84,113,126,165,252,263,287],"handle":[38,167],"as":[39,61,63,114],"sequence":[40,218,231,284],"size":[41],"increases.":[42],"This":[43],"makes":[44],"the":[45,75,79,105,133,149,187,193,197,202,236,242,250,254],"case":[46],"for":[47,92,213,279],"parallelization.":[48],"Parallelization":[49],"can":[50],"be":[51],"achieved":[52,190],"by":[53],"way":[54],"of":[55,78,132,177,204,219,238,285],"networked":[56],"platforms":[57,207,273],"(clusters,":[58],"grids,":[59],"etc)":[60],"well":[62],"using":[64,205,271],"modern":[65],"day":[66],"multi-core":[67,206,261,272],"chips.":[68],"METHODS:":[69],"In":[70],"this":[71,246],"paper,":[72],"we":[73],"exploit":[74,104],"parallelism":[76,128,159,195],"capabilities":[77],"IBM":[80,150,255],"Cell":[81,151,256],"Broadband":[82,257],"Engine":[83,258],"parallelize":[85],"an":[86],"algorithm":[91,162],"secondary":[94,290],"prediction.":[96],"We":[97,135],"design":[98],"three":[99],"different":[100],"implementation":[101],"strategies":[102],"that":[103,157],"inherent":[106,194],"data,":[107],"code":[108],"and/or":[109],"hybrid":[110],"parallelism,":[111],"referred":[112],"C-Par,":[115],"D-Par":[116],"H-Par,":[118],"analyze":[120],"their":[121],"performances.":[122],"Our":[123,154],"approach":[124],"attempts":[125],"introduce":[127],"critical":[130],"sections":[131],"algorithm.":[134],"ran":[136],"our":[137,239],"experiments":[138],"on":[139,148],"SONY":[140],"Play":[141],"Station":[142],"3":[143],"(PS3),":[144],"which":[145,170],"based":[147],"chip.":[152],"RESULTS:":[153],"results":[155,184,268],"suggest":[156],"introducing":[158],"DP":[161],"allows":[163],"it":[164],"easily":[166],"longer":[168],"sequences":[169],"otherwise":[171],"would":[172],"consume":[173],"large":[175],"amount":[176],"time":[178],"single":[180],"core":[181],"computers.":[182],"further":[185],"demonstrate":[186],"speed-up":[188,223],"gain":[189],"exploiting":[192],"also":[200,269],"elicits":[201],"advantages":[203],"towards":[208,274],"designing":[209,275],"more":[210,276],"sophisticated":[211,277],"methodologies":[212,278],"handling":[214,280],"fairly":[216,282],"long":[217,283],"RNA.":[220],"CONCLUSION:":[221],"performance":[224],"reported":[225,244],"here":[226],"promising,":[228],"when":[230],"length":[232],"long.":[234],"To":[235],"best":[237],"survey,":[241],"work":[243],"paper":[247],"probably":[249],"first-of-its-kind":[251],"utilize":[253],"(a":[259],"heterogeneous":[260],"chip)":[262],"implement":[264],"DP.":[266],"encourage":[270],"predict":[288],"its":[289],"structure.":[291]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}