{"id":"https://openalex.org/W2139493897","doi":"https://doi.org/10.1145/2631921","title":"Composable Modular Models for Synthetic Biology","display_name":"Composable Modular Models for Synthetic Biology","publication_year":2014,"publication_date":"2014-12-30","ids":{"openalex":"https://openalex.org/W2139493897","doi":"https://doi.org/10.1145/2631921","mag":"2139493897"},"language":"en","primary_location":{"id":"doi:10.1145/2631921","is_oa":true,"landing_page_url":"https://doi.org/10.1145/2631921","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/2631921","source":{"id":"https://openalex.org/S96198239","display_name":"ACM Journal on Emerging Technologies in Computing Systems","issn_l":"1550-4832","issn":["1550-4832","1550-4840"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Journal on Emerging Technologies in Computing Systems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://dl.acm.org/doi/pdf/10.1145/2631921","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028639846","display_name":"G\u00f6ksel M\u0131s\u0131rl\u0131","orcid":"https://orcid.org/0000-0002-2454-7188"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Goksel Misirli","raw_affiliation_strings":["Newcastle University, Newcastle upon Tyne, NE1 7RU, UK","Newcastle University , Newcastle upon Tyne, NE1 7RU , UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Newcastle University, Newcastle upon Tyne, NE1 7RU, UK","institution_ids":["https://openalex.org/I84884186"]},{"raw_affiliation_string":"Newcastle University , Newcastle upon Tyne, NE1 7RU , UK","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040063046","display_name":"Jennifer Hallinan","orcid":"https://orcid.org/0000-0002-2860-1022"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jennifer Hallinan","raw_affiliation_strings":["Newcastle University, Newcastle upon Tyne, NE1 7RU, UK","Newcastle University , Newcastle upon Tyne, NE1 7RU , UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Newcastle University, Newcastle upon Tyne, NE1 7RU, UK","institution_ids":["https://openalex.org/I84884186"]},{"raw_affiliation_string":"Newcastle University , Newcastle upon Tyne, NE1 7RU , UK","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089978830","display_name":"Anil Wipat","orcid":"https://orcid.org/0000-0001-7310-4191"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Anil Wipat","raw_affiliation_strings":["Newcastle University, Newcastle upon Tyne, NE1 7RU, UK","Newcastle University , Newcastle upon Tyne, NE1 7RU , UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Newcastle University, Newcastle upon Tyne, NE1 7RU, UK","institution_ids":["https://openalex.org/I84884186"]},{"raw_affiliation_string":"Newcastle University , Newcastle upon Tyne, NE1 7RU , UK","institution_ids":["https://openalex.org/I84884186"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.5693,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.67998067,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"11","issue":"3","first_page":"1","last_page":"19"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9936000108718872,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9729999899864197,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/modular-design","display_name":"Modular design","score":0.8197411894798279},{"id":"https://openalex.org/keywords/synthetic-biology","display_name":"Synthetic biology","score":0.6796464920043945},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6788396835327148},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4683358669281006},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.4628635346889496},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.36852800846099854},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3583550453186035},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.352356493473053},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.2947828769683838},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.29063528776168823},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14701437950134277}],"concepts":[{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.8197411894798279},{"id":"https://openalex.org/C191908910","wikidata":"https://www.wikidata.org/wiki/Q862838","display_name":"Synthetic biology","level":2,"score":0.6796464920043945},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6788396835327148},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4683358669281006},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.4628635346889496},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.36852800846099854},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3583550453186035},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.352356493473053},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2947828769683838},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.29063528776168823},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14701437950134277},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/2631921","is_oa":true,"landing_page_url":"https://doi.org/10.1145/2631921","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/2631921","source":{"id":"https://openalex.org/S96198239","display_name":"ACM Journal on Emerging Technologies in Computing Systems","issn_l":"1550-4832","issn":["1550-4832","1550-4840"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Journal on Emerging Technologies in Computing Systems","raw_type":"journal-article"},{"id":"pmh:oai:eprint.ncl.ac.uk:207076","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402485","display_name":"Newcastle University ePrints (Newcastle Univesity)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I84884186","host_organization_name":"Newcastle University","host_organization_lineage":["https://openalex.org/I84884186"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""}],"best_oa_location":{"id":"doi:10.1145/2631921","is_oa":true,"landing_page_url":"https://doi.org/10.1145/2631921","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/2631921","source":{"id":"https://openalex.org/S96198239","display_name":"ACM Journal on Emerging Technologies in Computing Systems","issn_l":"1550-4832","issn":["1550-4832","1550-4840"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Journal on Emerging Technologies in Computing Systems","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4399999976158142,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G2932300532","display_name":null,"funder_award_id":"EP/J02175X/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G4197673415","display_name":null,"funder_award_id":"EP/J02175X","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G4841078542","display_name":"Sandpit: The Programmable Rhizosphere","funder_award_id":"EP/H019162/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G7034511799","display_name":"An infrastructure for platform technology in synthetic biology","funder_award_id":"EP/J02175X/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2139493897.pdf","grobid_xml":"https://content.openalex.org/works/W2139493897.grobid-xml"},"referenced_works_count":74,"referenced_works":["https://openalex.org/W50265910","https://openalex.org/W78674370","https://openalex.org/W783868446","https://openalex.org/W1525281610","https://openalex.org/W1532739430","https://openalex.org/W1553203915","https://openalex.org/W1597538863","https://openalex.org/W1599969036","https://openalex.org/W1603293791","https://openalex.org/W1645305843","https://openalex.org/W1853858368","https://openalex.org/W1967668980","https://openalex.org/W1972306691","https://openalex.org/W1982834739","https://openalex.org/W1994177537","https://openalex.org/W1999777663","https://openalex.org/W2008110239","https://openalex.org/W2008449595","https://openalex.org/W2013522363","https://openalex.org/W2022891974","https://openalex.org/W2029237398","https://openalex.org/W2034375827","https://openalex.org/W2046355391","https://openalex.org/W2047360542","https://openalex.org/W2057608747","https://openalex.org/W2060184615","https://openalex.org/W2061234822","https://openalex.org/W2061425021","https://openalex.org/W2070962276","https://openalex.org/W2073151461","https://openalex.org/W2078444049","https://openalex.org/W2078638493","https://openalex.org/W2078847148","https://openalex.org/W2080233018","https://openalex.org/W2083284116","https://openalex.org/W2084405349","https://openalex.org/W2097210022","https://openalex.org/W2101506009","https://openalex.org/W2102653059","https://openalex.org/W2104810358","https://openalex.org/W2108329085","https://openalex.org/W2110690451","https://openalex.org/W2112005387","https://openalex.org/W2114124738","https://openalex.org/W2114176419","https://openalex.org/W2114942707","https://openalex.org/W2117364474","https://openalex.org/W2121318645","https://openalex.org/W2121826976","https://openalex.org/W2121988991","https://openalex.org/W2123171788","https://openalex.org/W2134582538","https://openalex.org/W2139511723","https://openalex.org/W2144736357","https://openalex.org/W2147306790","https://openalex.org/W2149526286","https://openalex.org/W2150908245","https://openalex.org/W2158979830","https://openalex.org/W2161783808","https://openalex.org/W2162144833","https://openalex.org/W2166222448","https://openalex.org/W2166499263","https://openalex.org/W2167378214","https://openalex.org/W2167879794","https://openalex.org/W2168142693","https://openalex.org/W2169360734","https://openalex.org/W2169929748","https://openalex.org/W2170122529","https://openalex.org/W2317498462","https://openalex.org/W2325072505","https://openalex.org/W2335196113","https://openalex.org/W2527193322","https://openalex.org/W2771299811","https://openalex.org/W4246066782"],"related_works":["https://openalex.org/W1987791267","https://openalex.org/W2998813341","https://openalex.org/W1587227328","https://openalex.org/W2888805005","https://openalex.org/W2160425906","https://openalex.org/W1596201972","https://openalex.org/W1967954938","https://openalex.org/W1965688652","https://openalex.org/W229104840","https://openalex.org/W3216010002"],"abstract_inverted_index":{"Modelling":[0],"and":[1,44,82,96,115,173],"computational":[2,185],"simulation":[3],"are":[4,41,70,103],"crucial":[5],"for":[6,160],"the":[7,16,55,64,93,121,141,154],"large-scale":[8],"engineering":[9],"of":[10,57,72,110,123,128,130,156,177],"biological":[11,94],"circuits":[12,59],"since":[13],"they":[14],"allow":[15,181],"system":[17],"under":[18],"design":[19,33,51,143,186],"to":[20,24,91,135,152,180],"be":[21,113],"simulated":[22],"prior":[23],"implementation":[25],"in":[26,38,105,140],"vivo":[27,106],".":[28,107],"To":[29],"support":[30,136,153],"automated,":[31],"model-driven":[32,142],"it":[34,87],"is":[35,88,133],"desirable":[36,90],"that":[37,98],"silico":[39],"models":[40,109,132,159,179],"modular,":[42],"composable":[43],"use":[45,183],"standard":[46],"formats.":[47],"The":[48,126],"synthetic":[49,161],"biology":[50],"process":[52,122],"typically":[53],"involves":[54],"composition":[56],"genetic":[58,73],"from":[60],"individual":[61],"parts.":[62],"At":[63],"most":[65],"basic":[66],"level,":[67],"these":[68,101,178],"parts":[69,102,111],"representations":[71],"features":[74],"such":[75],"as":[76],"promoters,":[77],"ribosome":[78],"binding":[79],"sites":[80],"(RBSs),":[81],"coding":[83],"sequences":[84],"(CDSs).":[85],"However,":[86],"also":[89],"model":[92],"molecules":[95],"behaviour":[97],"arise":[99],"when":[100],"combined":[104],"Modular":[108],"can":[112],"composed":[114],"their":[116,182],"associated":[117],"systems":[118],"simulated,":[119],"facilitating":[120],"model-centred":[124],"design.":[125],"availability":[127],"databases":[129],"modular":[131,158],"essential":[134],"software":[137],"tools":[138],"used":[139],"process.":[144],"In":[145],"this":[146],"article,":[147],"we":[148],"present":[149],"an":[150],"approach":[151],"development":[155],"composable,":[157],"biology,":[162],"termed":[163],"Standard":[164],"Virtual":[165],"Parts.":[166],"We":[167],"then":[168],"describe":[169],"a":[170],"programmatically":[171],"accessible":[172],"publicly":[174],"available":[175],"database":[176],"by":[184],"tools.":[187]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
