{"id":"https://openalex.org/W1971548821","doi":"https://doi.org/10.1109/cdc.2013.6760079","title":"An in silico modeling toolbox for rapid prototyping of circuits in a biomolecular “breadboard” system","display_name":"An in silico modeling toolbox for rapid prototyping of circuits in a biomolecular “breadboard” system","publication_year":2013,"publication_date":"2013-12-01","ids":{"openalex":"https://openalex.org/W1971548821","doi":"https://doi.org/10.1109/cdc.2013.6760079","mag":"1971548821"},"language":"en","primary_location":{"id":"doi:10.1109/cdc.2013.6760079","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cdc.2013.6760079","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"52nd IEEE Conference on Decision and Control","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/A5052164947","display_name":"Zolt\u00e1n A. Tuza","orcid":"https://orcid.org/0000-0003-2896-1527"},"institutions":[{"id":"https://openalex.org/I31882830","display_name":"P\u00e1zm\u00e1ny P\u00e9ter Catholic University","ror":"https://ror.org/05v9kya57","country_code":"HU","type":"education","lineage":["https://openalex.org/I31882830"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"Zoltan A. Tuza","raw_affiliation_strings":["Faculty of Information Technology, PPCU, Budapest, Hungary","Fac. of Inf. Technol., PPCU, Budapest, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Information Technology, PPCU, Budapest, Hungary","institution_ids":["https://openalex.org/I31882830"]},{"raw_affiliation_string":"Fac. of Inf. Technol., PPCU, Budapest, Hungary","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068601494","display_name":"Vipul Singhal","orcid":"https://orcid.org/0000-0003-1670-1824"},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vipul Singhal","raw_affiliation_strings":["Department of Computation and Neural Systems","Dept. of Comput. & Neural Syst., California Inst. of Technol., Pasadena, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computation and Neural Systems","institution_ids":[]},{"raw_affiliation_string":"Dept. of Comput. & Neural Syst., California Inst. of Technol., Pasadena, CA, USA","institution_ids":["https://openalex.org/I122411786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100334905","display_name":"Jongmin Kim","orcid":"https://orcid.org/0000-0002-2713-1006"},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jongmin Kim","raw_affiliation_strings":["Department of Bioengineering","Dept. of Bioeng., California Inst. of Technol., Pasadena, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering","institution_ids":[]},{"raw_affiliation_string":"Dept. of Bioeng., California Inst. of Technol., Pasadena, CA, USA","institution_ids":["https://openalex.org/I122411786"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068600217","display_name":"Richard M. Murray","orcid":"https://orcid.org/0000-0002-5785-7481"},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard M. Murray","raw_affiliation_strings":["Department of Bioengineering","Dept. of Bioeng., California Inst. of Technol., Pasadena, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering","institution_ids":[]},{"raw_affiliation_string":"Dept. of Bioeng., California Inst. of Technol., Pasadena, CA, USA","institution_ids":["https://openalex.org/I122411786"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":13.3285,"has_fulltext":false,"cited_by_count":26,"citation_normalized_percentile":{"value":0.98855466,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"1404","last_page":"1410"},"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9921000003814697,"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":0.9800999760627747,"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/breadboard","display_name":"Breadboard","score":0.9629367589950562},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.893520176410675},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.725239634513855},{"id":"https://openalex.org/keywords/matlab","display_name":"MATLAB","score":0.5430490374565125},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.4964483380317688},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.42228758335113525},{"id":"https://openalex.org/keywords/rapid-prototyping","display_name":"Rapid prototyping","score":0.42062586545944214},{"id":"https://openalex.org/keywords/control-engineering","display_name":"Control engineering","score":0.3548567295074463},{"id":"https://openalex.org/keywords/computer-engineering","display_name":"Computer engineering","score":0.3477720022201538},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.3236082196235657},{"id":"https://openalex.org/keywords/electronic-engineering","display_name":"Electronic engineering","score":0.2190605103969574},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1736011505126953},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10651594400405884}],"concepts":[{"id":"https://openalex.org/C14116294","wikidata":"https://www.wikidata.org/wiki/Q174334","display_name":"Breadboard","level":2,"score":0.9629367589950562},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.893520176410675},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.725239634513855},{"id":"https://openalex.org/C2780365114","wikidata":"https://www.wikidata.org/wiki/Q169478","display_name":"MATLAB","level":2,"score":0.5430490374565125},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.4964483380317688},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.42228758335113525},{"id":"https://openalex.org/C2780395129","wikidata":"https://www.wikidata.org/wiki/Q1128971","display_name":"Rapid prototyping","level":2,"score":0.42062586545944214},{"id":"https://openalex.org/C133731056","wikidata":"https://www.wikidata.org/wiki/Q4917288","display_name":"Control engineering","level":1,"score":0.3548567295074463},{"id":"https://openalex.org/C113775141","wikidata":"https://www.wikidata.org/wiki/Q428691","display_name":"Computer engineering","level":1,"score":0.3477720022201538},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.3236082196235657},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.2190605103969574},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1736011505126953},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10651594400405884},{"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},{"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/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cdc.2013.6760079","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cdc.2013.6760079","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"52nd IEEE Conference on Decision and Control","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1761088907","https://openalex.org/W1963611162","https://openalex.org/W1967459725","https://openalex.org/W1969015205","https://openalex.org/W1973577260","https://openalex.org/W1973873896","https://openalex.org/W1974156076","https://openalex.org/W1978151264","https://openalex.org/W1985161570","https://openalex.org/W1995780830","https://openalex.org/W1999679140","https://openalex.org/W2024991751","https://openalex.org/W2037913229","https://openalex.org/W2041166318","https://openalex.org/W2047882868","https://openalex.org/W2053614105","https://openalex.org/W2079056664","https://openalex.org/W2104586872","https://openalex.org/W2108407690","https://openalex.org/W2111497213","https://openalex.org/W2113555445","https://openalex.org/W2147775831","https://openalex.org/W2148641266","https://openalex.org/W2151282396","https://openalex.org/W2153067536","https://openalex.org/W2156021274","https://openalex.org/W2157507882","https://openalex.org/W2213968760","https://openalex.org/W2308740962","https://openalex.org/W2324786322","https://openalex.org/W2327010950","https://openalex.org/W4249304522"],"related_works":["https://openalex.org/W2153067536","https://openalex.org/W1976865287","https://openalex.org/W2071463351","https://openalex.org/W1967459725","https://openalex.org/W2327010950","https://openalex.org/W1973873896","https://openalex.org/W2087993212","https://openalex.org/W1974156076","https://openalex.org/W2147775831","https://openalex.org/W2134759932","https://openalex.org/W2121998297","https://openalex.org/W2950851734","https://openalex.org/W1975379503","https://openalex.org/W1971439989","https://openalex.org/W2146561267","https://openalex.org/W2124013800","https://openalex.org/W2001426985","https://openalex.org/W2012114611","https://openalex.org/W1645305843","https://openalex.org/W1587481053"],"abstract_inverted_index":{"In":[0],"this":[1],"paper,":[2],"we":[3],"develop":[4],"an":[5,12,15],"experimentally":[6],"validated":[7],"MATLAB":[8],"software":[9],"toolbox":[10,23,59],"as":[11],"accompaniment":[13],"to":[14,50,55,80],"in":[16,32,74],"vitro":[17],"cell-free":[18,34,75],"biomolecular":[19,72],"\u201cbreadboard\u201d":[20],"system.":[21],"The":[22,58],"gives":[24],"insight":[25],"into":[26],"the":[27,33,44],"dynamics":[28],"of":[29],"unmeasured":[30],"states":[31],"system,":[35],"accounting":[36],"especially":[37],"for":[38,64,70],"resource":[39],"usage.":[40],"Parameter":[41],"lumping":[42],"and":[43,54,67],"reduced":[45],"order":[46],"modeling":[47,69],"are":[48],"used":[49],"maintain":[51],"computational":[52],"tractability":[53],"avoid":[56],"ill-conditioning.":[57],"provides":[60],"a":[61],"general":[62],"framework":[63],"experiment":[65],"planning":[66],"predictive":[68],"synthetic":[71],"circuits":[73,83],"systems,":[76],"accelerating":[77],"our":[78],"capacity":[79],"rationally":[81],"design":[82],"from":[84],"well":[85],"characterized":[86],"parts.":[87]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}