{"id":"https://openalex.org/W2063213764","doi":"https://doi.org/10.1109/fpt.2007.4439249","title":"A Framework for Implementing a Network-Based Stochastic Biochemical Simulator on an FPGA","display_name":"A Framework for Implementing a Network-Based Stochastic Biochemical Simulator on an FPGA","publication_year":2007,"publication_date":"2007-12-01","ids":{"openalex":"https://openalex.org/W2063213764","doi":"https://doi.org/10.1109/fpt.2007.4439249","mag":"2063213764"},"language":"en","primary_location":{"id":"doi:10.1109/fpt.2007.4439249","is_oa":false,"landing_page_url":"https://doi.org/10.1109/fpt.2007.4439249","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 International Conference on Field-Programmable Technology","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/A5011990551","display_name":"Masato Yoshimi","orcid":"https://orcid.org/0000-0003-1343-9795"},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Masato Yoshimi","raw_affiliation_strings":["Dept. of Computer Science, Keio University, Yokohama, Japan","Keio University, Yokohama#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Keio University, Yokohama, Japan","institution_ids":["https://openalex.org/I203951103"]},{"raw_affiliation_string":"Keio University, Yokohama#TAB#","institution_ids":["https://openalex.org/I203951103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030966571","display_name":"Yuri Nishikawa","orcid":"https://orcid.org/0000-0001-9957-2727"},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yuri Nishikawa","raw_affiliation_strings":["Dept. of Computer Science, Keio University, Yokohama, Japan","Keio University, Yokohama#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Keio University, Yokohama, Japan","institution_ids":["https://openalex.org/I203951103"]},{"raw_affiliation_string":"Keio University, Yokohama#TAB#","institution_ids":["https://openalex.org/I203951103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111486521","display_name":"Toshinori Kojima","orcid":null},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Toshinori Kojima","raw_affiliation_strings":["Dept. of Computer Science, Keio University, Yokohama, Japan","Keio University, Yokohama#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Keio University, Yokohama, Japan","institution_ids":["https://openalex.org/I203951103"]},{"raw_affiliation_string":"Keio University, Yokohama#TAB#","institution_ids":["https://openalex.org/I203951103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035967296","display_name":"Yasunori Osana","orcid":"https://orcid.org/0009-0006-2099-6708"},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yasunori Osana","raw_affiliation_strings":["Dept. of Computer Science, Keio University, Yokohama, Japan","Keio University, Yokohama#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Keio University, Yokohama, Japan","institution_ids":["https://openalex.org/I203951103"]},{"raw_affiliation_string":"Keio University, Yokohama#TAB#","institution_ids":["https://openalex.org/I203951103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008451312","display_name":"Akira Funahashi","orcid":"https://orcid.org/0000-0003-0605-239X"},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Akira Funahashi","raw_affiliation_strings":["Dept. of Computer Science, Keio University, Yokohama, Japan","Keio University, Yokohama#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Keio University, Yokohama, Japan","institution_ids":["https://openalex.org/I203951103"]},{"raw_affiliation_string":"Keio University, Yokohama#TAB#","institution_ids":["https://openalex.org/I203951103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089950523","display_name":"Noriko Hiroi","orcid":"https://orcid.org/0000-0002-0214-373X"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Noriko Hiroi","raw_affiliation_strings":["ENMBL-EBI, Thornton group, European Bioinformatics Institude, Cambridge, UK","European Bioinformatics Institude, ENMBL-EBI, Thornton group, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10, 1SD, UK. E-mail: bio@am.ics.keio.ac.jp"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ENMBL-EBI, Thornton group, European Bioinformatics Institude, Cambridge, UK","institution_ids":["https://openalex.org/I1303153112"]},{"raw_affiliation_string":"European Bioinformatics Institude, ENMBL-EBI, Thornton group, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10, 1SD, UK. E-mail: bio@am.ics.keio.ac.jp","institution_ids":["https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106183057","display_name":"Yuichiro Shibata","orcid":null},"institutions":[{"id":"https://openalex.org/I43777268","display_name":"Nagasaki University","ror":"https://ror.org/058h74p94","country_code":"JP","type":"education","lineage":["https://openalex.org/I43777268"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yuichiro Shibata","raw_affiliation_strings":["Dept. of Computer and Information Sciences, Nagasaki University, Nagasaki, Japan","Dept. of Computer and Information Sciences, Nagasaki University, Nagasaki, 852-8521 Japan. E-mail: bio@am.ics.keio.ac.jp"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer and Information Sciences, Nagasaki University, Nagasaki, Japan","institution_ids":["https://openalex.org/I43777268"]},{"raw_affiliation_string":"Dept. of Computer and Information Sciences, Nagasaki University, Nagasaki, 852-8521 Japan. E-mail: bio@am.ics.keio.ac.jp","institution_ids":["https://openalex.org/I43777268"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065425806","display_name":"Hideki Yamada","orcid":null},"institutions":[{"id":"https://openalex.org/I43777268","display_name":"Nagasaki University","ror":"https://ror.org/058h74p94","country_code":"JP","type":"education","lineage":["https://openalex.org/I43777268"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hideki Yamada","raw_affiliation_strings":["Dept. of Computer and Information Sciences, Nagasaki University, Nagasaki, Japan","Dept. of Computer and Information Sciences, Nagasaki University, Nagasaki, 852-8521 Japan. E-mail: bio@am.ics.keio.ac.jp"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer and Information Sciences, Nagasaki University, Nagasaki, Japan","institution_ids":["https://openalex.org/I43777268"]},{"raw_affiliation_string":"Dept. of Computer and Information Sciences, Nagasaki University, Nagasaki, 852-8521 Japan. E-mail: bio@am.ics.keio.ac.jp","institution_ids":["https://openalex.org/I43777268"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086835862","display_name":"Hiroaki Kitano","orcid":"https://orcid.org/0000-0002-3589-1953"},"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":"Hiroaki Kitano","raw_affiliation_strings":["Kitano Symbiotic Systems Project, Japan Science and Technology Agency, Tokyo, Japan","Kitano Symbiotic Systems Project, ERATO-SORST, Japan Science and Technology Agency, Tokyo, 150-0001 Japan. E-mail: bio@am.ics.keio.ac.jp"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Kitano Symbiotic Systems Project, Japan Science and Technology Agency, Tokyo, Japan","institution_ids":["https://openalex.org/I4210086780"]},{"raw_affiliation_string":"Kitano Symbiotic Systems Project, ERATO-SORST, Japan Science and Technology Agency, Tokyo, 150-0001 Japan. E-mail: bio@am.ics.keio.ac.jp","institution_ids":["https://openalex.org/I4210086780"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112796185","display_name":"Hideharu Amano","orcid":null},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hideharu Amano","raw_affiliation_strings":["Dept. of Computer Science, Keio University, Yokohama, Japan","Dept. of Computer Science, Keio University, Yokohama, 223-8522, Japan. E-mail: bio@am.ics.keio.ac.jp"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Keio University, Yokohama, Japan","institution_ids":["https://openalex.org/I203951103"]},{"raw_affiliation_string":"Dept. of Computer Science, Keio University, Yokohama, 223-8522, Japan. E-mail: bio@am.ics.keio.ac.jp","institution_ids":["https://openalex.org/I203951103"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5011990551"],"corresponding_institution_ids":["https://openalex.org/I203951103"],"apc_list":null,"apc_paid":null,"fwci":0.2691,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.5888268,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"193","last_page":"200"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"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/T10904","display_name":"Embedded Systems Design Techniques","score":0.9904000163078308,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9506000280380249,"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":0.8228307962417603},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.8145512342453003},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.8136532306671143},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6292376518249512},{"id":"https://openalex.org/keywords/interconnection","display_name":"Interconnection","score":0.5970653891563416},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.589321494102478},{"id":"https://openalex.org/keywords/network-simulation","display_name":"Network simulation","score":0.4566227197647095},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.37477752566337585},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.3228576183319092},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.27091702818870544},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.16480740904808044},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1404988169670105}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8228307962417603},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.8145512342453003},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.8136532306671143},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6292376518249512},{"id":"https://openalex.org/C123745756","wikidata":"https://www.wikidata.org/wiki/Q1665949","display_name":"Interconnection","level":2,"score":0.5970653891563416},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.589321494102478},{"id":"https://openalex.org/C139940560","wikidata":"https://www.wikidata.org/wiki/Q290036","display_name":"Network simulation","level":2,"score":0.4566227197647095},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.37477752566337585},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3228576183319092},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.27091702818870544},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.16480740904808044},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1404988169670105},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/fpt.2007.4439249","is_oa":false,"landing_page_url":"https://doi.org/10.1109/fpt.2007.4439249","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 International Conference on Field-Programmable Technology","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":8,"referenced_works":["https://openalex.org/W1963855808","https://openalex.org/W2042321087","https://openalex.org/W2072670807","https://openalex.org/W2078734278","https://openalex.org/W2102653059","https://openalex.org/W2112764635","https://openalex.org/W2125381698","https://openalex.org/W6677198229"],"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/W2013643406","https://openalex.org/W2027972911","https://openalex.org/W2157978810","https://openalex.org/W2076915000","https://openalex.org/W2765822612"],"abstract_inverted_index":{"This":[0],"paper":[1],"studies":[2],"several":[3,32],"designs":[4],"of":[5,9,24],"network-based":[6],"FPGA":[7],"implementation":[8],"a":[10,57],"stochastic":[11],"simulation":[12],"algorithm":[13],"called":[14],"the":[15],"next":[16],"reaction":[17],"method,":[18],"known":[19],"for":[20],"its":[21],"large":[22],"number":[23],"calculation":[25],"involved.":[26],"The":[27],"procedure":[28],"is":[29],"divided":[30],"into":[31],"subdivisions":[33],"which":[34],"will":[35],"be":[36],"implemented":[37],"as":[38,50],"independent":[39],"modules,":[40],"and":[41],"they":[42],"are":[43],"connected":[44],"with":[45,66],"configurable":[46],"interconnection":[47],"networks":[48],"so":[49],"to":[51],"provide":[52],"high":[53],"throughput.":[54],"By":[55],"performing":[56],"multi-threading":[58],"simulation,":[59],"3.6":[60],"times":[61],"speedup":[62],"was":[63],"obtained":[64],"compared":[65],"an":[67],"execution":[68],"on":[69],"general":[70],"purpose":[71],"processors.":[72]},"counts_by_year":[],"updated_date":"2026-05-05T08:41:31.759640","created_date":"2025-10-10T00:00:00"}
