{"id":"https://openalex.org/W7204868567","doi":"https://doi.org/10.5281/zenodo.22231345","title":"Cells Running Our Software: A Contemporary Synthesis Review of Synthetic Biology and the Design of Living Circuits","display_name":"Cells Running Our Software: A Contemporary Synthesis Review of Synthetic Biology and the Design of Living Circuits","publication_year":2026,"publication_date":"2026-09-01","ids":{"openalex":"https://openalex.org/W7204868567","doi":"https://doi.org/10.5281/zenodo.22231345"},"language":"en","primary_location":{"id":"doi:10.5281/zenodo.22231345","doi":"https://doi.org/10.5281/zenodo.22231345","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22231345","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"JournalArticle"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.5281/zenodo.22231345","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5120933120","display_name":"Zen Revista","orcid":"https://orcid.org/0009-0007-6299-2008","observed_orcids":["https://orcid.org/0009-0007-6299-2008"]},"institutions":[{"id":"https://openalex.org/I4210124990","display_name":"Faculdades Guarulhos","ror":"https://ror.org/02s6maw65","country_code":"BR","type":"other","lineage":["https://openalex.org/I4210124990"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Revista, Zen","raw_affiliation_strings":["Faculdade de Guarulhos (FG)"],"raw_orcid":"https://orcid.org/0009-0007-6299-2008","affiliations":[{"raw_affiliation_string":"Faculdade de Guarulhos (FG)","institution_ids":["https://openalex.org/I4210124990"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5148935964","display_name":"10 BIOLOGY","orcid":"https://orcid.org/0009-0007-6299-2008","observed_orcids":["https://orcid.org/0009-0007-6299-2008"]},"institutions":[{"id":"https://openalex.org/I4210124990","display_name":"Faculdades Guarulhos","ror":"https://ror.org/02s6maw65","country_code":"BR","type":"other","lineage":["https://openalex.org/I4210124990"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"BIOLOGY, 10","raw_affiliation_strings":["Faculdade de Guarulhos (FG)"],"raw_orcid":"https://orcid.org/0009-0007-6299-2008","affiliations":[{"raw_affiliation_string":"Faculdade de Guarulhos (FG)","institution_ids":["https://openalex.org/I4210124990"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210124990"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9657999873161316,"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":0.9657999873161316,"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":0.015300000086426735,"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/T10778","display_name":"Philosophy of Biology and Scientific Explanation","score":0.008100000210106373,"subfield":{"id":"https://openalex.org/subfields/1207","display_name":"History and Philosophy of Science"},"field":{"id":"https://openalex.org/fields/12","display_name":"Arts and Humanities"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/synthetic-biology","display_name":"synthetic biology","score":1.0},{"id":"https://openalex.org/keywords/synthetic-gene-circuits","display_name":"synthetic gene circuits","score":0.9190000295639038},{"id":"https://openalex.org/keywords/history-of-synthetic-biology","display_name":"history of synthetic biology","score":0.8190000057220459},{"id":"https://openalex.org/keywords/definitional-disputes","display_name":"definitional disputes","score":0.7680000066757202},{"id":"https://openalex.org/keywords/methodological-pluralism","display_name":"methodological pluralism","score":0.8830000162124634},{"id":"https://openalex.org/keywords/data-intensive-science","display_name":"data-intensive research","score":0.5879999995231628},{"id":"https://openalex.org/keywords/publication-practices","display_name":"publication practices","score":0.6079999804496765},{"id":"https://openalex.org/keywords/research-organization","display_name":"research organization","score":0.43700000643730164},{"id":"https://openalex.org/keywords/integrative-research-design","display_name":"integrative research design","score":0.8309999704360962}],"concepts":[{"id":"https://openalex.org/C191908910","wikidata":"https://www.wikidata.org/wiki/Q862838","display_name":"Synthetic biology","level":2,"score":0.6782000064849854},{"id":"https://openalex.org/C108154423","wikidata":"https://www.wikidata.org/wiki/Q1469792","display_name":"Salience (neuroscience)","level":2,"score":0.5717999935150146},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.5325000286102295},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5321000218391418},{"id":"https://openalex.org/C55587333","wikidata":"https://www.wikidata.org/wiki/Q1133029","display_name":"Engineering ethics","level":1,"score":0.5198000073432922},{"id":"https://openalex.org/C199033989","wikidata":"https://www.wikidata.org/wiki/Q1318295","display_name":"Narrative","level":2,"score":0.46619999408721924},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.4458000063896179},{"id":"https://openalex.org/C2776184637","wikidata":"https://www.wikidata.org/wiki/Q6506039","display_name":"Living systems","level":2,"score":0.41780000925064087},{"id":"https://openalex.org/C14224292","wikidata":"https://www.wikidata.org/wiki/Q13600188","display_name":"Conceptual framework","level":2,"score":0.3977999985218048},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.39079999923706055},{"id":"https://openalex.org/C7991579","wikidata":"https://www.wikidata.org/wiki/Q17955","display_name":"Criticism","level":2,"score":0.3869999945163727},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3603000044822693},{"id":"https://openalex.org/C18762648","wikidata":"https://www.wikidata.org/wiki/Q42213","display_name":"Work (physics)","level":2,"score":0.3495999872684479},{"id":"https://openalex.org/C49831778","wikidata":"https://www.wikidata.org/wiki/Q879021","display_name":"Pluralism (philosophy)","level":2,"score":0.3402999937534332},{"id":"https://openalex.org/C188147891","wikidata":"https://www.wikidata.org/wiki/Q147638","display_name":"Cognitive science","level":1,"score":0.3353999853134155},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.32580000162124634},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2791000008583069},{"id":"https://openalex.org/C36289849","wikidata":"https://www.wikidata.org/wiki/Q34749","display_name":"Social science","level":1,"score":0.26179999113082886},{"id":"https://openalex.org/C2781316041","wikidata":"https://www.wikidata.org/wiki/Q1230584","display_name":"Diversity (politics)","level":2,"score":0.26010000705718994},{"id":"https://openalex.org/C2992077199","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biological sciences","level":2,"score":0.2517000138759613}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.5281/zenodo.22231345","doi":"https://doi.org/10.5281/zenodo.22231345","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22231345","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"JournalArticle"},{"id":"doi:10.5281/zenodo.22231346","doi":"https://doi.org/10.5281/zenodo.22231346","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22231346","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"JournalArticle"},{"id":"doi:10.5281/zenodo.22311147","doi":"https://doi.org/10.5281/zenodo.22311147","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22311147","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"JournalArticle"},{"id":"doi:10.5281/zenodo.22311148","doi":"https://doi.org/10.5281/zenodo.22311148","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22311148","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"JournalArticle"},{"id":"doi:10.5281/zenodo.22606985","doi":"https://doi.org/10.5281/zenodo.22606985","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22606985","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"JournalArticle"},{"id":"doi:10.5281/zenodo.22606986","doi":"https://doi.org/10.5281/zenodo.22606986","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22606986","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"JournalArticle"}],"best_oa_location":{"id":"doi:10.5281/zenodo.22231345","doi":"https://doi.org/10.5281/zenodo.22231345","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22231345","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"JournalArticle"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W7204874497","https://openalex.org/W7207710510","https://openalex.org/W7206175396","https://openalex.org/W7206201331","https://openalex.org/W7204867462","https://openalex.org/W7204728857","https://openalex.org/W2002227368","https://openalex.org/W7204911445","https://openalex.org/W7204895559","https://openalex.org/W7204758541"],"abstract_inverted_index":{"This":[0],"article":[1,195],"presents":[2],"a":[3,145,149,200,206],"narrative":[4],"review":[5,51,126],"of":[6,12,18,47,56,75,99,156,162,184],"Synthetic":[7],"Biology":[8],"and":[9,38,63,70,84,102,108,151,181,186,205],"the":[10,16,50,53,57,60,72,78,85,97,110,131,152,157,160,182],"Design":[11],"Living":[13],"Circuits":[14],"in":[15,210],"context":[17],"Biology.":[19,211],"The":[20,125,194],"literature":[21,132],"on":[22,43,189],"this":[23],"topic":[24,158],"has":[25],"expanded":[26],"substantially":[27],"over":[28],"recent":[29],"decades,":[30],"yet":[31],"it":[32],"remains":[33],"fragmented":[34],"across":[35],"subfields,":[36],"methods,":[37],"national":[39],"research":[40,117,176],"traditions.":[41],"Drawing":[42],"an":[44],"interpretive":[45],"synthesis":[46,179],"representative":[48],"contributions,":[49],"reconstructs":[52],"historical":[54],"development":[55],"area,":[58],"examines":[59],"conceptual":[61,165],"foundations":[62],"definitional":[64,185],"disputes":[65],"that":[66,88],"organize":[67],"its":[68,163],"debates,":[69],"maps":[71],"contemporary":[73],"landscape":[74],"research,":[76],"including":[77],"methodological":[79,139],"shift":[80],"toward":[81],"data-intensive":[82],"approaches":[83],"institutional":[86],"pressures":[87],"shape":[89],"publication":[90],"practice.":[91],"Particular":[92],"attention":[93],"is":[94,133,141,172,196],"given":[95],"to":[96,109],"role":[98],"synthetic":[100,129],"biology":[101],"genetic":[103],"circuits":[104],"as":[105,144,148,198],"organizing":[106],"themes,":[107],"conditions":[111],"under":[112],"which":[113,190],"findings":[114],"from":[115],"different":[116],"traditions":[118],"can":[119],"be":[120],"brought":[121],"into":[122],"productive":[123],"comparison.":[124],"identifies":[127],"three":[128],"conclusions:":[130],"cumulatively":[134],"strong":[135],"but":[136],"organizationally":[137],"weak;":[138],"pluralism":[140],"better":[142],"understood":[143],"resource":[146],"than":[147],"defect;":[150],"growing":[153],"practical":[154],"salience":[155],"raises":[159],"stakes":[161],"unresolved":[164],"questions.":[166],"An":[167],"agenda":[168],"for":[169,203,208],"future":[170],"work":[171,188],"proposed,":[173],"emphasizing":[174],"integrative":[175],"designs,":[177],"transparent":[178],"practices,":[180],"protection":[183],"infrastructural":[187],"cumulative":[191],"progress":[192],"depends.":[193],"intended":[197],"both":[199],"reference":[201],"map":[202],"newcomers":[204],"provocation":[207],"specialists":[209]},"counts_by_year":[],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2026-09-02T00:00:00"}