{"id":"https://openalex.org/W2114627379","doi":"https://doi.org/10.1007/s11047-004-2644-9","title":"Development, evaluation and benchmarking of simulation software for biomolecule-based computing","display_name":"Development, evaluation and benchmarking of simulation software for biomolecule-based computing","publication_year":2004,"publication_date":"2004-12-01","ids":{"openalex":"https://openalex.org/W2114627379","doi":"https://doi.org/10.1007/s11047-004-2644-9","mag":"2114627379"},"language":"en","primary_location":{"id":"doi:10.1007/s11047-004-2644-9","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s11047-004-2644-9","pdf_url":null,"source":{"id":"https://openalex.org/S149828480","display_name":"Natural Computing","issn_l":"1567-7818","issn":["1567-7818","1572-9796"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Natural Computing","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/A5064124513","display_name":"Derrel Blain","orcid":null},"institutions":[{"id":"https://openalex.org/I94658018","display_name":"University of Memphis","ror":"https://ror.org/01cq23130","country_code":"US","type":"education","lineage":["https://openalex.org/I94658018"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Derrel Blain","raw_affiliation_strings":["Computer Science Division, The University of Memphis, Memphis, TN, 38152-3240, U.S.A","Computer Science Division, The University of Memphis, Memphis, U.S.A 38152-3240"],"affiliations":[{"raw_affiliation_string":"Computer Science Division, The University of Memphis, Memphis, TN, 38152-3240, U.S.A","institution_ids":["https://openalex.org/I94658018"]},{"raw_affiliation_string":"Computer Science Division, The University of Memphis, Memphis, U.S.A 38152-3240","institution_ids":["https://openalex.org/I94658018"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006855445","display_name":"Max Garz\u00f3n","orcid":"https://orcid.org/0000-0001-9552-2255"},"institutions":[{"id":"https://openalex.org/I94658018","display_name":"University of Memphis","ror":"https://ror.org/01cq23130","country_code":"US","type":"education","lineage":["https://openalex.org/I94658018"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Max Garzon","raw_affiliation_strings":["Computer Science Division, The University of Memphis, Memphis, TN, 38152-3240, U.S.A","Computer Science Division, The University of Memphis, Memphis, U.S.A 38152-3240"],"affiliations":[{"raw_affiliation_string":"Computer Science Division, The University of Memphis, Memphis, TN, 38152-3240, U.S.A","institution_ids":["https://openalex.org/I94658018"]},{"raw_affiliation_string":"Computer Science Division, The University of Memphis, Memphis, U.S.A 38152-3240","institution_ids":["https://openalex.org/I94658018"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009019474","display_name":"Soo-Yong Shin","orcid":"https://orcid.org/0000-0002-2410-6120"},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Soo-Yong Shin","raw_affiliation_strings":["Biointelligence Lab, School of Computer Science and Engineering, Seoul National University, Seoul, 151-742, Korea","Biointelligence Lab, School of Computer Science and Engineering, Seoul National University, Seoul, Korea 151-742#TAB#"],"affiliations":[{"raw_affiliation_string":"Biointelligence Lab, School of Computer Science and Engineering, Seoul National University, Seoul, 151-742, Korea","institution_ids":["https://openalex.org/I139264467"]},{"raw_affiliation_string":"Biointelligence Lab, School of Computer Science and Engineering, Seoul National University, Seoul, Korea 151-742#TAB#","institution_ids":["https://openalex.org/I139264467"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107826037","display_name":"Byoung\u2010Tak Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Byoung-Tak Zhang","raw_affiliation_strings":["Biointelligence Lab, School of Computer Science and Engineering, Seoul National University, Seoul, 151-742, Korea","Biointelligence Lab, School of Computer Science and Engineering, Seoul National University, Seoul, Korea 151-742#TAB#"],"affiliations":[{"raw_affiliation_string":"Biointelligence Lab, School of Computer Science and Engineering, Seoul National University, Seoul, 151-742, Korea","institution_ids":["https://openalex.org/I139264467"]},{"raw_affiliation_string":"Biointelligence Lab, School of Computer Science and Engineering, Seoul National University, Seoul, Korea 151-742#TAB#","institution_ids":["https://openalex.org/I139264467"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055668237","display_name":"Satoshi Kashiwamura","orcid":null},"institutions":[{"id":"https://openalex.org/I205349734","display_name":"Hokkaido University","ror":"https://ror.org/02e16g702","country_code":"JP","type":"education","lineage":["https://openalex.org/I205349734"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Satoshi Kashiwamura","raw_affiliation_strings":["Graduate School of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, 060-8628, Japan","Graduate School of Engineering, Hokkaido University, Sapporo, Japan 060-8628#TAB#"],"affiliations":[{"raw_affiliation_string":"Graduate School of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, 060-8628, Japan","institution_ids":["https://openalex.org/I205349734"]},{"raw_affiliation_string":"Graduate School of Engineering, Hokkaido University, Sapporo, Japan 060-8628#TAB#","institution_ids":["https://openalex.org/I205349734"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101572257","display_name":"Masahito Yamamoto","orcid":"https://orcid.org/0000-0002-7326-3691"},"institutions":[{"id":"https://openalex.org/I4210135477","display_name":"Arab Foundations Forum","ror":"https://ror.org/03y00r958","country_code":"JO","type":"nonprofit","lineage":["https://openalex.org/I4210135477"]},{"id":"https://openalex.org/I4210086780","display_name":"Japan Science and Technology Agency","ror":"https://ror.org/00097mb19","country_code":"JP","type":"government","lineage":["https://openalex.org/I4210086780"]},{"id":"https://openalex.org/I205349734","display_name":"Hokkaido University","ror":"https://ror.org/02e16g702","country_code":"JP","type":"education","lineage":["https://openalex.org/I205349734"]}],"countries":["JO","JP"],"is_corresponding":false,"raw_author_name":"Masahito Yamamoto","raw_affiliation_strings":["Graduate School of Information Science and Technology, Hokkaido University, North 14, West 9, Kita-ku, Sapporo, 060-0814, Japan","Japan Science and Technology Corporation (JST), CREST, Japan","Aff4 Aff5#TAB#"],"affiliations":[{"raw_affiliation_string":"Graduate School of Information Science and Technology, Hokkaido University, North 14, West 9, Kita-ku, Sapporo, 060-0814, Japan","institution_ids":["https://openalex.org/I205349734"]},{"raw_affiliation_string":"Japan Science and Technology Corporation (JST), CREST, Japan","institution_ids":["https://openalex.org/I4210086780"]},{"raw_affiliation_string":"Aff4 Aff5#TAB#","institution_ids":["https://openalex.org/I4210135477"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111969429","display_name":"Atsushi Kameda","orcid":null},"institutions":[{"id":"https://openalex.org/I4210086780","display_name":"Japan Science and Technology Agency","ror":"https://ror.org/00097mb19","country_code":"JP","type":"government","lineage":["https://openalex.org/I4210086780"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Atsushi Kameda","raw_affiliation_strings":["Japan Science and Technology Corporation (JST), CREST, Japan","Japan Science and Technology Corporation (JST), CREST, Japan#TAB#"],"affiliations":[{"raw_affiliation_string":"Japan Science and Technology Corporation (JST), CREST, Japan","institution_ids":["https://openalex.org/I4210086780"]},{"raw_affiliation_string":"Japan Science and Technology Corporation (JST), CREST, Japan#TAB#","institution_ids":["https://openalex.org/I4210086780"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043496932","display_name":"Azuma Ohuchi","orcid":null},"institutions":[{"id":"https://openalex.org/I4210135477","display_name":"Arab Foundations Forum","ror":"https://ror.org/03y00r958","country_code":"JO","type":"nonprofit","lineage":["https://openalex.org/I4210135477"]},{"id":"https://openalex.org/I4210086780","display_name":"Japan Science and Technology Agency","ror":"https://ror.org/00097mb19","country_code":"JP","type":"government","lineage":["https://openalex.org/I4210086780"]},{"id":"https://openalex.org/I205349734","display_name":"Hokkaido University","ror":"https://ror.org/02e16g702","country_code":"JP","type":"education","lineage":["https://openalex.org/I205349734"]}],"countries":["JO","JP"],"is_corresponding":false,"raw_author_name":"Azuma Ohuchi","raw_affiliation_strings":["Graduate School of Information Science and Technology, Hokkaido University, North 14, West 9, Kita-ku, Sapporo, 060-0814, Japan","Japan Science and Technology Corporation (JST), CREST, Japan","Aff4 Aff5#TAB#"],"affiliations":[{"raw_affiliation_string":"Graduate School of Information Science and Technology, Hokkaido University, North 14, West 9, Kita-ku, Sapporo, 060-0814, Japan","institution_ids":["https://openalex.org/I205349734"]},{"raw_affiliation_string":"Japan Science and Technology Corporation (JST), CREST, Japan","institution_ids":["https://openalex.org/I4210086780"]},{"raw_affiliation_string":"Aff4 Aff5#TAB#","institution_ids":["https://openalex.org/I4210135477"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5064124513"],"corresponding_institution_ids":["https://openalex.org/I94658018"],"apc_list":{"value":2290,"currency":"EUR","value_usd":2890},"apc_paid":null,"fwci":0.479,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.62448951,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"3","issue":"4","first_page":"427","last_page":"442"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","score":0.9998999834060669,"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/T12029","display_name":"DNA and Biological Computing","score":0.9998999834060669,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9993000030517578,"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/T12784","display_name":"Modular Robots and Swarm Intelligence","score":0.9954000115394592,"subfield":{"id":"https://openalex.org/subfields/2210","display_name":"Mechanical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7795053124427795},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.672805905342102},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5680442452430725},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5626102089881897},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5445500016212463},{"id":"https://openalex.org/keywords/software-development","display_name":"Software development","score":0.4587109684944153},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.4468362629413605},{"id":"https://openalex.org/keywords/software-framework","display_name":"Software framework","score":0.412739098072052},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.40245702862739563},{"id":"https://openalex.org/keywords/software-construction","display_name":"Software construction","score":0.3566606342792511},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.16990095376968384},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.11490949988365173}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7795053124427795},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.672805905342102},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5680442452430725},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5626102089881897},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5445500016212463},{"id":"https://openalex.org/C529173508","wikidata":"https://www.wikidata.org/wiki/Q638608","display_name":"Software development","level":3,"score":0.4587109684944153},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4468362629413605},{"id":"https://openalex.org/C76518257","wikidata":"https://www.wikidata.org/wiki/Q271680","display_name":"Software framework","level":5,"score":0.412739098072052},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.40245702862739563},{"id":"https://openalex.org/C186846655","wikidata":"https://www.wikidata.org/wiki/Q3398377","display_name":"Software construction","level":4,"score":0.3566606342792511},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.16990095376968384},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.11490949988365173},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"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/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/s11047-004-2644-9","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s11047-004-2644-9","pdf_url":null,"source":{"id":"https://openalex.org/S149828480","display_name":"Natural Computing","issn_l":"1567-7818","issn":["1567-7818","1572-9796"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Natural Computing","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320308928","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W11317389","https://openalex.org/W25287847","https://openalex.org/W66302005","https://openalex.org/W79218528","https://openalex.org/W127054358","https://openalex.org/W202717924","https://openalex.org/W242446277","https://openalex.org/W1510923188","https://openalex.org/W1516677870","https://openalex.org/W1554442128","https://openalex.org/W1566694705","https://openalex.org/W1576874705","https://openalex.org/W1582738019","https://openalex.org/W1780765560","https://openalex.org/W1782124149","https://openalex.org/W1977312644","https://openalex.org/W2031214412","https://openalex.org/W2072834565","https://openalex.org/W2096307073","https://openalex.org/W2494487823","https://openalex.org/W2571967924","https://openalex.org/W2752491485","https://openalex.org/W4235299643","https://openalex.org/W4235535825","https://openalex.org/W4236360615","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W4214835859","https://openalex.org/W4312927049","https://openalex.org/W2380017313","https://openalex.org/W2520111506","https://openalex.org/W2368462085","https://openalex.org/W2359960837","https://openalex.org/W2366623749","https://openalex.org/W2026093893","https://openalex.org/W2523959329","https://openalex.org/W2519691570"],"abstract_inverted_index":null,"counts_by_year":[{"year":2014,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
