{"id":"https://openalex.org/W2108403211","doi":"https://doi.org/10.1109/csb.2003.1227404","title":"Implementing parallel hmm-pfam on the EARTH multithreaded architecture","display_name":"Implementing parallel hmm-pfam on the EARTH multithreaded architecture","publication_year":2004,"publication_date":"2004-03-30","ids":{"openalex":"https://openalex.org/W2108403211","doi":"https://doi.org/10.1109/csb.2003.1227404","mag":"2108403211"},"language":"en","primary_location":{"id":"doi:10.1109/csb.2003.1227404","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2003.1227404","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","raw_type":"proceedings-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/A5051986607","display_name":"Weirong Zhu","orcid":null},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"W. Zhu","raw_affiliation_strings":["Department of Electrical & Computer Engineering, University of Delaware, USA","Dept. of Electr. & Comput. Eng., Delaware Univ., Newark, DE, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical & Computer Engineering, University of Delaware, USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Dept. of Electr. & Comput. Eng., Delaware Univ., Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101472379","display_name":"Yanwei Niu","orcid":"https://orcid.org/0000-0002-1492-1340"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Y. Niu","raw_affiliation_strings":["Department of Electrical & Computer Engineering, University of Delaware, USA","Dept. of Electr. & Comput. Eng., Delaware Univ., Newark, DE, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical & Computer Engineering, University of Delaware, USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Dept. of Electr. & Comput. Eng., Delaware Univ., Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089094253","display_name":"Jue Lu","orcid":"https://orcid.org/0000-0001-8281-2720"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. Lu","raw_affiliation_strings":["Department of Electrical & Computer Engineering, University of Delaware, USA","Dept. of Electr. & Comput. Eng., Delaware Univ., Newark, DE, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical & Computer Engineering, University of Delaware, USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Dept. of Electr. & Comput. Eng., Delaware Univ., Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046024163","display_name":"Guang R. Gao","orcid":"https://orcid.org/0000-0002-5265-7528"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"G.R. Gao","raw_affiliation_strings":["Department of Electrical & Computer Engineering, University of Delaware, USA","Dept. of Electr. & Comput. Eng., Delaware Univ., Newark, DE, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical & Computer Engineering, University of Delaware, USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Dept. of Electr. & Comput. Eng., Delaware Univ., Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5051986607"],"corresponding_institution_ids":["https://openalex.org/I86501945"],"apc_list":null,"apc_paid":null,"fwci":0.6029,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.65659987,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"549","last_page":"550"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9952999949455261,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9945999979972839,"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":0.8629506826400757},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.8513460159301758},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.7637954950332642},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.7210092544555664},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.5459063649177551},{"id":"https://openalex.org/keywords/multithreading","display_name":"Multithreading","score":0.5095062851905823},{"id":"https://openalex.org/keywords/event","display_name":"Event (particle physics)","score":0.46817082166671753},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.46260106563568115},{"id":"https://openalex.org/keywords/cluster","display_name":"Cluster (spacecraft)","score":0.45064741373062134},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.24165523052215576},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.20055094361305237}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8629506826400757},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.8513460159301758},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7637954950332642},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7210092544555664},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5459063649177551},{"id":"https://openalex.org/C201410400","wikidata":"https://www.wikidata.org/wiki/Q1064412","display_name":"Multithreading","level":3,"score":0.5095062851905823},{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.46817082166671753},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.46260106563568115},{"id":"https://openalex.org/C164866538","wikidata":"https://www.wikidata.org/wiki/Q367351","display_name":"Cluster (spacecraft)","level":2,"score":0.45064741373062134},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.24165523052215576},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.20055094361305237},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C138101251","wikidata":"https://www.wikidata.org/wiki/Q213092","display_name":"Thread (computing)","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/csb.2003.1227404","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2003.1227404","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.138.4393","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.138.4393","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://csdl.computer.org/comp/proceedings/csb/2003/2000/00/20000549.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.4699999988079071}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W101030905","https://openalex.org/W2141885858","https://openalex.org/W2151831732","https://openalex.org/W4229779965","https://openalex.org/W6676368354","https://openalex.org/W7037405753"],"related_works":["https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W2146343568","https://openalex.org/W98480971","https://openalex.org/W2150291671","https://openalex.org/W3089117407","https://openalex.org/W3138386522","https://openalex.org/W2499279132","https://openalex.org/W2023373638","https://openalex.org/W3090445364"],"abstract_inverted_index":{"Hmmpfam":[0],"is":[1,23,64],"a":[2,14,51,61],"widely":[3],"used":[4],"computation-intensive":[5],"bioinformatics":[6],"software":[7],"for":[8],"sequence":[9],"classification.":[10],"This":[11],"poster":[12],"describes":[13],"new":[15],"parallel":[16],"implementation":[17,38,41],"of":[18,34,53,60],"hmmpfam":[19],"on":[20,45],"EARTH,":[21],"which":[22],"an":[24],"event-driven":[25],"fine-grain":[26],"multithreaded":[27],"programming":[28],"execution":[29,58],"model.":[30],"The":[31],"comparison":[32],"results":[33],"the":[35,57],"original":[36],"PVM":[37],"and":[39,48],"our":[40],"shows":[42],"notable":[43],"improvements":[44],"absolute":[46],"speedup":[47],"scalability.":[49],"On":[50],"cluster":[52],"128":[54],"dual-CPU":[55],"nodes,":[56],"time":[59],"representative":[62],"testbench":[63],"reduced":[65],"from":[66],"15.9":[67],"hours":[68],"to":[69],"4.3":[70],"minutes.":[71]},"counts_by_year":[{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
