{"id":"https://openalex.org/W1987019839","doi":"https://doi.org/10.1109/biocas.2013.6679717","title":"EDA inspired open-source framework for synthetic biology","display_name":"EDA inspired open-source framework for synthetic biology","publication_year":2013,"publication_date":"2013-10-01","ids":{"openalex":"https://openalex.org/W1987019839","doi":"https://doi.org/10.1109/biocas.2013.6679717","mag":"1987019839"},"language":"en","primary_location":{"id":"doi:10.1109/biocas.2013.6679717","is_oa":false,"landing_page_url":"https://doi.org/10.1109/biocas.2013.6679717","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 IEEE Biomedical Circuits and Systems Conference (BioCAS)","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/A5106483571","display_name":"Morgan Madec","orcid":"https://orcid.org/0000-0001-9537-642X"},"institutions":[{"id":"https://openalex.org/I4210100283","display_name":"Laboratoire des Sciences de l'Ing\u00e9nieur, de l'Informatique et de l'Imagerie","ror":"https://ror.org/00k4e5n71","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I2801509770","https://openalex.org/I4210095849","https://openalex.org/I4210100283","https://openalex.org/I4210159245","https://openalex.org/I68947357"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Morgan Madec","raw_affiliation_strings":["Laboratoire des sciences, de l'Ing\u00e9nieur de l'Informatique et de l'Imagerie-Equipe Syst\u00e8mes et Microsyst\u00e8mes H\u00e9t\u00e9rog\u00e8nes, ILLKIRCH CEDEX, France","Lab. des Sci. de l'Ingenieur, de l'Inf. et de l'Imagerie, Equipe Syst. et Microsystemes Heterogenes, Illkirch, France"],"affiliations":[{"raw_affiliation_string":"Laboratoire des sciences, de l'Ing\u00e9nieur de l'Informatique et de l'Imagerie-Equipe Syst\u00e8mes et Microsyst\u00e8mes H\u00e9t\u00e9rog\u00e8nes, ILLKIRCH CEDEX, France","institution_ids":["https://openalex.org/I4210100283"]},{"raw_affiliation_string":"Lab. des Sci. de l'Ingenieur, de l'Inf. et de l'Imagerie, Equipe Syst. et Microsystemes Heterogenes, Illkirch, France","institution_ids":["https://openalex.org/I4210100283"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023748893","display_name":"Fran\u00e7ois P\u00eacheux","orcid":"https://orcid.org/0000-0002-4118-8690"},"institutions":[{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Francois Pecheux","raw_affiliation_strings":["Laboratoire d'Informatique Paris VI-Equipe Architecture et Logiciels pour les Syst\u00e8mes Embarqu\u00e9s sur Puce, PARIS CEDEX 05, France","Equipe Archit. et Logiciels pour les Syst. Embarques sur Puce, Lab. d'Inf. Paris VI, Paris, France"],"affiliations":[{"raw_affiliation_string":"Laboratoire d'Informatique Paris VI-Equipe Architecture et Logiciels pour les Syst\u00e8mes Embarqu\u00e9s sur Puce, PARIS CEDEX 05, France","institution_ids":["https://openalex.org/I39804081"]},{"raw_affiliation_string":"Equipe Archit. et Logiciels pour les Syst. Embarques sur Puce, Lab. d'Inf. Paris VI, Paris, France","institution_ids":["https://openalex.org/I39804081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021308987","display_name":"Yves Gendrault","orcid":null},"institutions":[{"id":"https://openalex.org/I4210100283","display_name":"Laboratoire des Sciences de l'Ing\u00e9nieur, de l'Informatique et de l'Imagerie","ror":"https://ror.org/00k4e5n71","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I2801509770","https://openalex.org/I4210095849","https://openalex.org/I4210100283","https://openalex.org/I4210159245","https://openalex.org/I68947357"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Yves Gendrault","raw_affiliation_strings":["Laboratoire des sciences, de l'Ing\u00e9nieur de l'Informatique et de l'Imagerie-Equipe Syst\u00e8mes et Microsyst\u00e8mes H\u00e9t\u00e9rog\u00e8nes, ILLKIRCH CEDEX, France","Lab. des Sci. de l'Ingenieur, de l'Inf. et de l'Imagerie, Equipe Syst. et Microsystemes Heterogenes, Illkirch, France"],"affiliations":[{"raw_affiliation_string":"Laboratoire des sciences, de l'Ing\u00e9nieur de l'Informatique et de l'Imagerie-Equipe Syst\u00e8mes et Microsyst\u00e8mes H\u00e9t\u00e9rog\u00e8nes, ILLKIRCH CEDEX, France","institution_ids":["https://openalex.org/I4210100283"]},{"raw_affiliation_string":"Lab. des Sci. de l'Ingenieur, de l'Inf. et de l'Imagerie, Equipe Syst. et Microsystemes Heterogenes, Illkirch, France","institution_ids":["https://openalex.org/I4210100283"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033396547","display_name":"Loic Bauer","orcid":null},"institutions":[{"id":"https://openalex.org/I4210100283","display_name":"Laboratoire des Sciences de l'Ing\u00e9nieur, de l'Informatique et de l'Imagerie","ror":"https://ror.org/00k4e5n71","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I2801509770","https://openalex.org/I4210095849","https://openalex.org/I4210100283","https://openalex.org/I4210159245","https://openalex.org/I68947357"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Loic Bauer","raw_affiliation_strings":["Laboratoire des sciences, de l'Ing\u00e9nieur de l'Informatique et de l'Imagerie-Equipe Syst\u00e8mes et Microsyst\u00e8mes H\u00e9t\u00e9rog\u00e8nes, ILLKIRCH CEDEX, France","Lab. des Sci. de l'Ingenieur, de l'Inf. et de l'Imagerie, Equipe Syst. et Microsystemes Heterogenes, Illkirch, France"],"affiliations":[{"raw_affiliation_string":"Laboratoire des sciences, de l'Ing\u00e9nieur de l'Informatique et de l'Imagerie-Equipe Syst\u00e8mes et Microsyst\u00e8mes H\u00e9t\u00e9rog\u00e8nes, ILLKIRCH CEDEX, France","institution_ids":["https://openalex.org/I4210100283"]},{"raw_affiliation_string":"Lab. des Sci. de l'Ingenieur, de l'Inf. et de l'Imagerie, Equipe Syst. et Microsystemes Heterogenes, Illkirch, France","institution_ids":["https://openalex.org/I4210100283"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065266817","display_name":"Jacques Haiech","orcid":"https://orcid.org/0000-0003-2908-8053"},"institutions":[{"id":"https://openalex.org/I4210116974","display_name":"Laboratoire d'Innovation Th\u00e9rapeutique","ror":"https://ror.org/02g4mxc89","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I4210116974","https://openalex.org/I4210128300","https://openalex.org/I68947357"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Jacques Haiech","raw_affiliation_strings":["Laboratoire d'Innovations Th\u00e9rapeutiques, ILLKIRCH CEDEX","Lab. d'Innovations Therapeutiques (LIT), Illkirch, France"],"affiliations":[{"raw_affiliation_string":"Laboratoire d'Innovations Th\u00e9rapeutiques, ILLKIRCH CEDEX","institution_ids":["https://openalex.org/I4210116974"]},{"raw_affiliation_string":"Lab. d'Innovations Therapeutiques (LIT), Illkirch, France","institution_ids":["https://openalex.org/I4210116974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055580961","display_name":"Christophe Lallement","orcid":"https://orcid.org/0000-0002-0708-7212"},"institutions":[{"id":"https://openalex.org/I4210100283","display_name":"Laboratoire des Sciences de l'Ing\u00e9nieur, de l'Informatique et de l'Imagerie","ror":"https://ror.org/00k4e5n71","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I2801509770","https://openalex.org/I4210095849","https://openalex.org/I4210100283","https://openalex.org/I4210159245","https://openalex.org/I68947357"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Christophe Lallement","raw_affiliation_strings":["Laboratoire des sciences, de l'Ing\u00e9nieur de l'Informatique et de l'Imagerie-Equipe Syst\u00e8mes et Microsyst\u00e8mes H\u00e9t\u00e9rog\u00e8nes, ILLKIRCH CEDEX, France","Lab. des Sci. de l'Ingenieur, de l'Inf. et de l'Imagerie, Equipe Syst. et Microsystemes Heterogenes, Illkirch, France"],"affiliations":[{"raw_affiliation_string":"Laboratoire des sciences, de l'Ing\u00e9nieur de l'Informatique et de l'Imagerie-Equipe Syst\u00e8mes et Microsyst\u00e8mes H\u00e9t\u00e9rog\u00e8nes, ILLKIRCH CEDEX, France","institution_ids":["https://openalex.org/I4210100283"]},{"raw_affiliation_string":"Lab. des Sci. de l'Ingenieur, de l'Inf. et de l'Imagerie, Equipe Syst. et Microsystemes Heterogenes, Illkirch, France","institution_ids":["https://openalex.org/I4210100283"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5106483571"],"corresponding_institution_ids":["https://openalex.org/I4210100283"],"apc_list":null,"apc_paid":null,"fwci":0.5849,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.67172713,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"403","issue":null,"first_page":"374","last_page":"377"},"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9927999973297119,"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":0.953499972820282,"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/netlist","display_name":"Netlist","score":0.9652611017227173},{"id":"https://openalex.org/keywords/synthetic-biology","display_name":"Synthetic biology","score":0.735099196434021},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7298557162284851},{"id":"https://openalex.org/keywords/electronic-design-automation","display_name":"Electronic design automation","score":0.564049243927002},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.554818868637085},{"id":"https://openalex.org/keywords/automation","display_name":"Automation","score":0.5060240626335144},{"id":"https://openalex.org/keywords/systemc","display_name":"SystemC","score":0.5050023198127747},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.49506059288978577},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.4347715675830841},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.4161873459815979},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.39255809783935547},{"id":"https://openalex.org/keywords/systems-engineering","display_name":"Systems engineering","score":0.33403974771499634},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.2432767152786255},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.19747617840766907},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.17382767796516418},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15822818875312805},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.14229169487953186}],"concepts":[{"id":"https://openalex.org/C177650935","wikidata":"https://www.wikidata.org/wiki/Q1760303","display_name":"Netlist","level":2,"score":0.9652611017227173},{"id":"https://openalex.org/C191908910","wikidata":"https://www.wikidata.org/wiki/Q862838","display_name":"Synthetic biology","level":2,"score":0.735099196434021},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7298557162284851},{"id":"https://openalex.org/C64260653","wikidata":"https://www.wikidata.org/wiki/Q1194864","display_name":"Electronic design automation","level":2,"score":0.564049243927002},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.554818868637085},{"id":"https://openalex.org/C115901376","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automation","level":2,"score":0.5060240626335144},{"id":"https://openalex.org/C2776928060","wikidata":"https://www.wikidata.org/wiki/Q1753563","display_name":"SystemC","level":2,"score":0.5050023198127747},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.49506059288978577},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.4347715675830841},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.4161873459815979},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.39255809783935547},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.33403974771499634},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.2432767152786255},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.19747617840766907},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.17382767796516418},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15822818875312805},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.14229169487953186},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/biocas.2013.6679717","is_oa":false,"landing_page_url":"https://doi.org/10.1109/biocas.2013.6679717","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 IEEE Biomedical Circuits and Systems Conference (BioCAS)","raw_type":"proceedings-article"},{"id":"pmh:oai:HAL:hal-05395102v1","is_oa":false,"landing_page_url":"https://univoak.hal.science/hal-05395102","pdf_url":null,"source":{"id":"https://openalex.org/S4406922461","display_name":"SPIRE - Sciences Po Institutional REpository","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Biomedical Circuits and Systems Confrence (BIOCAS 2013), 2013, Rotterdam, Netherlands. pp.374-377, &#x27E8;10.1109/BioCAS.2013.6679717&#x27E9;","raw_type":"Conference papers"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1556762041","https://openalex.org/W1983914131","https://openalex.org/W2013234054","https://openalex.org/W2019954703","https://openalex.org/W2023873427","https://openalex.org/W2047882868","https://openalex.org/W2079549835","https://openalex.org/W2091731123","https://openalex.org/W2098390695","https://openalex.org/W2101506009","https://openalex.org/W2105662588","https://openalex.org/W2109906206","https://openalex.org/W2118849670","https://openalex.org/W2120435550","https://openalex.org/W2134759932","https://openalex.org/W2168493238","https://openalex.org/W6633457945"],"related_works":["https://openalex.org/W2170314243","https://openalex.org/W2119179026","https://openalex.org/W2794947590","https://openalex.org/W2114971758","https://openalex.org/W2109932036","https://openalex.org/W2098869417","https://openalex.org/W3012060364","https://openalex.org/W2106223679","https://openalex.org/W2503215586","https://openalex.org/W3214257365"],"abstract_inverted_index":{"The":[0,29,77],"topic":[1],"of":[2,18,36,45,56,85,92,97,109,131,145],"this":[3],"paper":[4],"is":[5,134],"to":[6,11,74,102],"develop":[7],"an":[8,154],"open-source":[9],"framework":[10,78,133],"help":[12],"bio-engineers":[13],"through":[14],"the":[15,33,37,46,83,86,95,98,106,127,132,150],"different":[16],"stages":[17,35],"a":[19,41,53,90,110,139,142],"top-down":[20],"design":[21],"process":[22],"for":[23,119],"new":[24],"artificial":[25],"biosystems":[26],"(synthetic":[27],"biology).":[28],"presented":[30],"tools":[31,70],"address":[32],"upstream":[34],"design,":[38],"starting":[39],"from":[40],"high-level":[42,87],"behavioral":[43],"description":[44,88],"targeted":[47],"biological":[48,151],"function":[49],"and":[50,105,136],"ending":[51],"with":[52,100,138],"working":[54],"assembly":[55],"abstract":[57],"BioBricks":[58,103],"performing":[59],"that":[60,64,115],"very":[61],"function.":[62],"For":[63],"purpose,":[65],"EDA":[66],"(Electronic":[67],"Design":[68],"Automation)":[69],"are":[71],"indeed":[72],"adapted":[73],"synthetic":[75],"biology.":[76],"involves":[79],"three":[80],"main":[81],"steps:":[82],"interpretation":[84],"into":[89],"netlist":[91,99,114],"logical":[93,143],"functions,":[94],"optimization":[96,124],"respect":[101],"capabilities":[104],"automated":[107],"generation":[108],"SystemC-AMS":[111],"abstracted":[112],"simulatable":[113],"can":[116],"be":[117],"used":[118],"further":[120],"analysis":[121],"(low-level":[122],"simulation,":[123],"...).":[125],"Throughout":[126],"paper,":[128],"each":[129],"stage":[130],"detailed":[135],"illustrated":[137],"simple":[140],"(from":[141,149],"point":[144],"view)":[146],"but":[147],"complex":[148],"viewpoint)":[152],"example:":[153],"in-vivo":[155],"chemical":[156],"species":[157],"regulation":[158],"system.":[159]},"counts_by_year":[{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
