{"id":"https://openalex.org/W2105764235","doi":"https://doi.org/10.1142/s0218126614500315","title":"FINE-GRAINED PARALLEL APPLICATION SPECIFIC COMPUTING FOR RNA SECONDARY STRUCTURE PREDICTION ON FPGA","display_name":"FINE-GRAINED PARALLEL APPLICATION SPECIFIC COMPUTING FOR RNA SECONDARY STRUCTURE PREDICTION ON FPGA","publication_year":2014,"publication_date":"2014-01-07","ids":{"openalex":"https://openalex.org/W2105764235","doi":"https://doi.org/10.1142/s0218126614500315","mag":"2105764235"},"language":"en","primary_location":{"id":"doi:10.1142/s0218126614500315","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0218126614500315","pdf_url":null,"source":{"id":"https://openalex.org/S167602672","display_name":"Journal of Circuits Systems and Computers","issn_l":"0218-1266","issn":["0218-1266","1793-6454"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319815","host_organization_name":"World Scientific","host_organization_lineage":["https://openalex.org/P4310319815"],"host_organization_lineage_names":["World Scientific"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Circuits, Systems and Computers","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079454573","display_name":"Zhu Qiang-hua","orcid":null},"institutions":[{"id":"https://openalex.org/I2800710378","display_name":"Naval University of Engineering","ror":"https://ror.org/056vyez31","country_code":"CN","type":"education","lineage":["https://openalex.org/I2800710378"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"QIANGHUA ZHU","raw_affiliation_strings":["Electronics Engineering College, Naval Engineering University, Wuhan 430033, China"],"affiliations":[{"raw_affiliation_string":"Electronics Engineering College, Naval Engineering University, Wuhan 430033, China","institution_ids":["https://openalex.org/I2800710378"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100676785","display_name":"Fei Xia","orcid":"https://orcid.org/0000-0003-4343-1444"},"institutions":[{"id":"https://openalex.org/I2800710378","display_name":"Naval University of Engineering","ror":"https://ror.org/056vyez31","country_code":"CN","type":"education","lineage":["https://openalex.org/I2800710378"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"FEI XIA","raw_affiliation_strings":["Electronics Engineering College, Naval Engineering University, Wuhan 430033, China"],"affiliations":[{"raw_affiliation_string":"Electronics Engineering College, Naval Engineering University, Wuhan 430033, China","institution_ids":["https://openalex.org/I2800710378"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5120165384","display_name":"Guoqing Jin","orcid":"https://orcid.org/0009-0001-7108-9159"},"institutions":[{"id":"https://openalex.org/I2800710378","display_name":"Naval University of Engineering","ror":"https://ror.org/056vyez31","country_code":"CN","type":"education","lineage":["https://openalex.org/I2800710378"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"GUOQING JIN","raw_affiliation_strings":["Electronics Engineering College, Naval Engineering University, Wuhan 430033, China"],"affiliations":[{"raw_affiliation_string":"Electronics Engineering College, Naval Engineering University, Wuhan 430033, China","institution_ids":["https://openalex.org/I2800710378"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5079454573"],"corresponding_institution_ids":["https://openalex.org/I2800710378"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.10625717,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"23","issue":"03","first_page":"1450031","last_page":"1450031"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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":1.0,"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/T11482","display_name":"RNA modifications and cancer","score":0.9988999962806702,"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":0.9984999895095825,"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":0.7980313897132874},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.6585103273391724},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6018897294998169},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.5554018020629883},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5498480796813965},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.5069561004638672},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.47271081805229187},{"id":"https://openalex.org/keywords/scheduling","display_name":"Scheduling (production processes)","score":0.4524870216846466},{"id":"https://openalex.org/keywords/reuse","display_name":"Reuse","score":0.4296317398548126},{"id":"https://openalex.org/keywords/dynamic-programming","display_name":"Dynamic programming","score":0.4247409701347351},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.2694607675075531},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.18558269739151},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.17843300104141235}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7980313897132874},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.6585103273391724},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6018897294998169},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.5554018020629883},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5498480796813965},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.5069561004638672},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.47271081805229187},{"id":"https://openalex.org/C206729178","wikidata":"https://www.wikidata.org/wiki/Q2271896","display_name":"Scheduling (production processes)","level":2,"score":0.4524870216846466},{"id":"https://openalex.org/C206588197","wikidata":"https://www.wikidata.org/wiki/Q846574","display_name":"Reuse","level":2,"score":0.4296317398548126},{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.4247409701347351},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.2694607675075531},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.18558269739151},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.17843300104141235},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1142/s0218126614500315","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0218126614500315","pdf_url":null,"source":{"id":"https://openalex.org/S167602672","display_name":"Journal of Circuits Systems and Computers","issn_l":"0218-1266","issn":["0218-1266","1793-6454"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319815","host_organization_name":"World Scientific","host_organization_lineage":["https://openalex.org/P4310319815"],"host_organization_lineage_names":["World Scientific"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Circuits, Systems and Computers","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.7300000190734863,"display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W1526127001","https://openalex.org/W1968245790","https://openalex.org/W1974597460","https://openalex.org/W2008907996","https://openalex.org/W2023074165","https://openalex.org/W2025763720","https://openalex.org/W2042844155","https://openalex.org/W2054926865","https://openalex.org/W2054931730","https://openalex.org/W2056737829","https://openalex.org/W2061384718","https://openalex.org/W2064345118","https://openalex.org/W2065735339","https://openalex.org/W2076580581","https://openalex.org/W2076756368","https://openalex.org/W2102046276","https://openalex.org/W2103250001","https://openalex.org/W2104141342","https://openalex.org/W2106293441","https://openalex.org/W2109297587","https://openalex.org/W2115275409","https://openalex.org/W2121918723","https://openalex.org/W2123241418","https://openalex.org/W2134489577","https://openalex.org/W2139138332","https://openalex.org/W2148599336"],"related_works":["https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W98480971","https://openalex.org/W2150291671","https://openalex.org/W17155033","https://openalex.org/W2027972911","https://openalex.org/W2146343568","https://openalex.org/W2013643406","https://openalex.org/W2157978810","https://openalex.org/W2597809628"],"abstract_inverted_index":{"RNA":[0,31,94,165,200],"secondary":[1,32],"structure":[2,33],"prediction":[3],"is":[4,18,45,153,210],"one":[5],"of":[6,48,69,116,148,176,206,214],"the":[7,19,38,46,55,67,73,117,137,146,154,184,203,215],"important":[8],"research":[9],"areas":[10],"in":[11,75,119],"modern":[12],"bioinformatics":[13],"and":[14,24,44,51,61,89,112,130],"computational":[15],"biology.":[16],"PKNOTS":[17,70,87],"most":[20],"famous":[21],"benchmark":[22],"program":[23],"has":[25],"been":[26],"widely":[27],"used":[28],"to":[29,135],"predict":[30],"including":[34,168],"pseudoknots.":[35,169],"It":[36],"adopts":[37],"standard":[39],"4D":[40,160],"dynamic":[41,161],"programming":[42,162],"method":[43],"basis":[47],"many":[49],"variants":[50],"improved":[52,104],"algorithms.":[53],"Unfortunately,":[54],"O(N":[56],"6":[57],")":[58],"computing":[59,114],"requirements":[60],"complicated":[62],"data":[63,105,125,127,141],"dependency":[64,128],"greatly":[65],"limits":[66],"usefulness":[68],"package":[71],"with":[72,192],"explosion":[74],"gene":[76],"database":[77],"size.":[78],"In":[79],"this":[80],"paper,":[81],"we":[82],"present":[83],"a":[84,174,189],"fine-grained":[85],"parallel":[86],"algorithm":[88],"prototype":[90],"system":[91],"for":[92,139,158,164,198],"accelerating":[93,159],"folding":[95,166],"application":[96,167],"on":[97,188],"field":[98],"programmable":[99],"gate-array":[100],"(FPGA)":[101],"platform.":[102],"We":[103,122],"locality":[106],"by":[107],"converting":[108],"cycle":[109],"nested":[110],"relationship":[111],"reorganizing":[113],"order":[115],"elements":[118],"source":[120],"code.":[121],"aggressively":[123],"exploit":[124],"reuse,":[126],"elimination":[129],"memory":[131],"access":[132],"scheduling":[133],"strategies":[134],"minimize":[136],"need":[138],"loading":[140],"from":[142],"external":[143],"memory.":[144],"To":[145],"best":[147],"our":[149,151,207],"knowledge,":[150],"design":[152],"first":[155],"FPGA":[156,208],"implementation":[157],"problem":[163],"The":[170],"experimental":[171],"results":[172],"show":[173],"factor":[175],"more":[177],"than":[178],"11":[179],"\u00d7":[180],"average":[181],"speedup":[182],"over":[183],"PKNOTS-1.05":[185],"software":[186],"running":[187],"PC":[190],"platform":[191],"AMD":[193],"Phenom":[194],"9650":[195],"Quad":[196],"CPU":[197],"input":[199],"sequences.":[201],"However,":[202],"power":[204],"consumption":[205],"accelerator":[209],"only":[211],"about":[212],"50%":[213],"general-purpose":[216],"micro-processors.":[217]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
