{"id":"https://openalex.org/W2040217848","doi":"https://doi.org/10.1109/icecs.2012.6463795","title":"A soft IP core generating SoCs for the efficient stochastic simulation of large Biomolecular Networks using FPGAs","display_name":"A soft IP core generating SoCs for the efficient stochastic simulation of large Biomolecular Networks using FPGAs","publication_year":2012,"publication_date":"2012-12-01","ids":{"openalex":"https://openalex.org/W2040217848","doi":"https://doi.org/10.1109/icecs.2012.6463795","mag":"2040217848"},"language":"en","primary_location":{"id":"doi:10.1109/icecs.2012.6463795","is_oa":false,"landing_page_url":"https://doi.org/10.1109/icecs.2012.6463795","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 19th IEEE International Conference on Electronics, Circuits, and Systems (ICECS 2012)","raw_type":"proceedings-article"},"type":"conference-paper","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/A5085387169","display_name":"Orsalia Hazapis","orcid":null},"institutions":[{"id":"https://openalex.org/I200777214","display_name":"National and Kapodistrian University of Athens","ror":"https://ror.org/04gnjpq42","country_code":"GR","type":"education","lineage":["https://openalex.org/I200777214"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Orsalia Georgia Hazapis","raw_affiliation_strings":["Graduate Program Information Technologies in Medicine and Biology, Department of Informatics and Telecommunications, University of Athens, Greece","Dept. Of Inf. & Telecommun., Univ. of Athens, Athens, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate Program Information Technologies in Medicine and Biology, Department of Informatics and Telecommunications, University of Athens, Greece","institution_ids":["https://openalex.org/I200777214"]},{"raw_affiliation_string":"Dept. Of Inf. & Telecommun., Univ. of Athens, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041636394","display_name":"Evangelos Logaras","orcid":"https://orcid.org/0000-0003-4921-3819"},"institutions":[{"id":"https://openalex.org/I200777214","display_name":"National and Kapodistrian University of Athens","ror":"https://ror.org/04gnjpq42","country_code":"GR","type":"education","lineage":["https://openalex.org/I200777214"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Evangelos Logaras","raw_affiliation_strings":["Graduate Program Information Technologies in Medicine and Biology, Department of Informatics and Telecommunications, University of Athens, Greece","Dept. Of Inf. & Telecommun., Univ. of Athens, Athens, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate Program Information Technologies in Medicine and Biology, Department of Informatics and Telecommunications, University of Athens, Greece","institution_ids":["https://openalex.org/I200777214"]},{"raw_affiliation_string":"Dept. Of Inf. & Telecommun., Univ. of Athens, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070325341","display_name":"\u0397\u03bb\u03af\u03b1\u03c2 \u03a3. \u039c\u03b1\u03bd\u03c9\u03bb\u03ac\u03ba\u03bf\u03c2","orcid":"https://orcid.org/0000-0001-6376-0419"},"institutions":[{"id":"https://openalex.org/I200777214","display_name":"National and Kapodistrian University of Athens","ror":"https://ror.org/04gnjpq42","country_code":"GR","type":"education","lineage":["https://openalex.org/I200777214"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Elias S. Manolakos","raw_affiliation_strings":["Graduate Program Information Technologies in Medicine and Biology, Department of Informatics and Telecommunications, University of Athens, Greece","Dept. Of Inf. & Telecommun., Univ. of Athens, Athens, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate Program Information Technologies in Medicine and Biology, Department of Informatics and Telecommunications, University of Athens, Greece","institution_ids":["https://openalex.org/I200777214"]},{"raw_affiliation_string":"Dept. Of Inf. & Telecommun., Univ. of Athens, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I200777214"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.13419675,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"24","issue":null,"first_page":"77","last_page":"80"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","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/T10621","display_name":"Gene Regulatory Network Analysis","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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9937999844551086,"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":0.987500011920929,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.7926141023635864},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7278562784194946},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.651189386844635},{"id":"https://openalex.org/keywords/ethernet","display_name":"Ethernet","score":0.6110939383506775},{"id":"https://openalex.org/keywords/vhdl","display_name":"VHDL","score":0.5858922600746155},{"id":"https://openalex.org/keywords/virtex","display_name":"Virtex","score":0.5293980836868286},{"id":"https://openalex.org/keywords/system-on-a-chip","display_name":"System on a chip","score":0.4162255525588989},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.3406044840812683},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.3099443018436432}],"concepts":[{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.7926141023635864},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7278562784194946},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.651189386844635},{"id":"https://openalex.org/C172173386","wikidata":"https://www.wikidata.org/wiki/Q79984","display_name":"Ethernet","level":2,"score":0.6110939383506775},{"id":"https://openalex.org/C36941000","wikidata":"https://www.wikidata.org/wiki/Q209455","display_name":"VHDL","level":3,"score":0.5858922600746155},{"id":"https://openalex.org/C2777674469","wikidata":"https://www.wikidata.org/wiki/Q20741011","display_name":"Virtex","level":3,"score":0.5293980836868286},{"id":"https://openalex.org/C118021083","wikidata":"https://www.wikidata.org/wiki/Q610398","display_name":"System on a chip","level":2,"score":0.4162255525588989},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.3406044840812683},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.3099443018436432}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/icecs.2012.6463795","is_oa":false,"landing_page_url":"https://doi.org/10.1109/icecs.2012.6463795","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 19th IEEE International Conference on Electronics, Circuits, and Systems (ICECS 2012)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","score":0.7300000190734863,"id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1992148609","https://openalex.org/W2005980128","https://openalex.org/W2011432832","https://openalex.org/W2034375827","https://openalex.org/W2042321087","https://openalex.org/W2078734278","https://openalex.org/W2093179886","https://openalex.org/W2101768141","https://openalex.org/W2110061820","https://openalex.org/W2112764635","https://openalex.org/W2119272407","https://openalex.org/W2121772137","https://openalex.org/W2125381698","https://openalex.org/W2139129111","https://openalex.org/W2150908245","https://openalex.org/W2508432680","https://openalex.org/W6678198832"],"related_works":["https://openalex.org/W3004362061","https://openalex.org/W4297665406","https://openalex.org/W2364622490","https://openalex.org/W2042515040","https://openalex.org/W2383986884","https://openalex.org/W2356141508","https://openalex.org/W2544043553","https://openalex.org/W2749962643","https://openalex.org/W2546284597","https://openalex.org/W2390807153"],"abstract_inverted_index":{"A":[0],"soft":[1],"IP":[2],"core,":[3],"expressed":[4],"in":[5,52],"parametric":[6],"VHDL,":[7],"has":[8],"been":[9],"developed":[10],"and":[11,49,76,81],"used":[12],"to":[13,42,45,58,87,106],"synthesize":[14],"different":[15],"multiprocessor":[16],"Systems":[17],"on":[18,31,119],"Chip":[19],"(SoCs)":[20],"for":[21,79],"the":[22,65,74,92,111],"stochastic":[23],"simulation":[24,97],"of":[25,64,109,113],"large-size":[26],"biochemical":[27],"reaction":[28],"networks":[29,55],"based":[30],"Gillespie's":[32],"First":[33],"Reaction":[34],"Method":[35],"(FRM).":[36],"The":[37,61],"SoCs":[38,66,94],"can":[39,95],"be":[40],"configured":[41],"have":[43],"up":[44,57,105],"N=8":[46],"Processing":[47],"Elements":[48],"simulate":[50],"efficiently":[51],"hardware":[53],"biomolecular":[54],"with":[56,69],"m=16K":[59],"reactions.":[60],"FPGA":[62,91],"implementations":[63],"are":[67],"communicating":[68],"a":[70,88],"host":[71],"PC":[72],"via":[73],"serial":[75],"Ethernet":[77],"ports":[78],"control":[80],"data":[82],"transmission":[83],"respectively.":[84],"When":[85],"mapped":[86],"Virtex-5":[89],"Xilinx":[90],"FRM":[93],"deliver":[96],"performance":[98,112],"(in":[99],"Mega-Reactions/sec)":[100],"that":[101],"may":[102],"exceed":[103],"by":[104],"two":[107],"orders":[108],"magnitude":[110],"well":[114],"known":[115],"software":[116],"simulators":[117],"running":[118],"fast":[120],"PCs.":[121]},"counts_by_year":[],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
