{"id":"https://openalex.org/W4225301751","doi":"https://doi.org/10.1371/journal.pcbi.1009987","title":"BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts","display_name":"BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts","publication_year":2022,"publication_date":"2022-04-20","ids":{"openalex":"https://openalex.org/W4225301751","doi":"https://doi.org/10.1371/journal.pcbi.1009987","pmid":"https://pubmed.ncbi.nlm.nih.gov/35442944"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1009987","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009987","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1009987","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022025721","display_name":"William Poole","orcid":"https://orcid.org/0000-0002-2958-6776"},"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":true,"raw_author_name":"William Poole","raw_affiliation_strings":["Computation and Neural Systems, California Institute of Technology, Pasadena, California, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-2958-6776","affiliations":[{"raw_affiliation_string":"Computation and Neural Systems, California Institute of Technology, Pasadena, California, United States of America","institution_ids":["https://openalex.org/I122411786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084734938","display_name":"Ayush Pandey","orcid":"https://orcid.org/0000-0003-3590-4459"},"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":"Ayush Pandey","raw_affiliation_strings":["Control and Dynamical Systems, California Institute of Technology, Pasadena, California, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-3590-4459","affiliations":[{"raw_affiliation_string":"Control and Dynamical Systems, California Institute of Technology, Pasadena, California, United States of America","institution_ids":["https://openalex.org/I122411786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070792009","display_name":"Andrey Shur","orcid":"https://orcid.org/0000-0001-9372-6713"},"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":"Andrey Shur","raw_affiliation_strings":["Bioengineering, California Institute of Technology, Pasadena, California, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-9372-6713","affiliations":[{"raw_affiliation_string":"Bioengineering, California Institute of Technology, Pasadena, California, United States of America","institution_ids":["https://openalex.org/I122411786"]}]},{"author_position":"middle","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/I4210092485","display_name":"Bioengineering (Switzerland)","ror":"https://ror.org/00m2xfz17","country_code":"CH","type":"company","lineage":["https://openalex.org/I4210092485"]},{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["CH","GB"],"is_corresponding":false,"raw_author_name":"Zoltan A. Tuza","raw_affiliation_strings":["Bioengineering, Imperial College London, London, England"],"raw_orcid":"https://orcid.org/0000-0003-2896-1527","affiliations":[{"raw_affiliation_string":"Bioengineering, Imperial College London, London, England","institution_ids":["https://openalex.org/I47508984","https://openalex.org/I4210092485"]}]},{"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":["Control and Dynamical Systems, California Institute of Technology, Pasadena, California, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-5785-7481","affiliations":[{"raw_affiliation_string":"Control and Dynamical Systems, California Institute of Technology, Pasadena, California, United States of America","institution_ids":["https://openalex.org/I122411786"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5022025721"],"corresponding_institution_ids":["https://openalex.org/I122411786"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.7359,"has_fulltext":true,"cited_by_count":29,"citation_normalized_percentile":{"value":0.84518579,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"18","issue":"4","first_page":"e1009987","last_page":"e1009987"},"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":0.9991000294685364,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9929999709129333,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.9733527302742004},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.8046887516975403},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8017964363098145},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7808040380477905},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.7620351314544678},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.7443333864212036},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.7338823080062866},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5540828704833984},{"id":"https://openalex.org/keywords/synthetic-biology","display_name":"Synthetic biology","score":0.5152443051338196},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5072681307792664},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.49880504608154297},{"id":"https://openalex.org/keywords/modelling-biological-systems","display_name":"Modelling biological systems","score":0.4954143762588501},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.43291565775871277},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.4067959189414978},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.327373206615448},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.18024176359176636},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.11061891913414001},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.10698175430297852},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09588176012039185}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9733527302742004},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.8046887516975403},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8017964363098145},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7808040380477905},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.7620351314544678},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.7443333864212036},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.7338823080062866},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5540828704833984},{"id":"https://openalex.org/C191908910","wikidata":"https://www.wikidata.org/wiki/Q862838","display_name":"Synthetic biology","level":2,"score":0.5152443051338196},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5072681307792664},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.49880504608154297},{"id":"https://openalex.org/C137866125","wikidata":"https://www.wikidata.org/wiki/Q4299308","display_name":"Modelling biological systems","level":3,"score":0.4954143762588501},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.43291565775871277},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.4067959189414978},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.327373206615448},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.18024176359176636},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.11061891913414001},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.10698175430297852},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09588176012039185}],"mesh":[{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1009987","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009987","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:35442944","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35442944","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:authors.library.caltech.edu:104725","is_oa":true,"landing_page_url":"https://authors.library.caltech.edu/104725/","pdf_url":"https://resolver.caltech.edu/CaltechAUTHORS:20200804-104555959","source":{"id":"https://openalex.org/S4306402161","display_name":"CaltechAUTHORS (California Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I122411786","host_organization_name":"California Institute of Technology","host_organization_lineage":["https://openalex.org/I122411786"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:19c214960dd94a4ca19891de3d5f1815","is_oa":true,"landing_page_url":"https://doaj.org/article/19c214960dd94a4ca19891de3d5f1815","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 18, Iss 4, p e1009987 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9060376","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9060376","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1009987","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009987","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G125688323","display_name":null,"funder_award_id":"HR0011-17-2-0008","funder_id":"https://openalex.org/F4320332180","funder_display_name":"Defense Advanced Research Projects Agency"},{"id":"https://openalex.org/G1326091714","display_name":null,"funder_award_id":"W911NF-19-2-0026","funder_id":"https://openalex.org/F4320338502","funder_display_name":"Institute for Collaborative Biotechnologies"},{"id":"https://openalex.org/G335602769","display_name":null,"funder_award_id":"Agreement HR0011-17-2-0008","funder_id":"https://openalex.org/F4320332180","funder_display_name":"Defense Advanced Research Projects Agency"},{"id":"https://openalex.org/G3712632952","display_name":null,"funder_award_id":"CBET-1903477","funder_id":"https://openalex.org/F4320337390","funder_display_name":"Division of Chemical, Bioengineering, Environmental, and Transport Systems"},{"id":"https://openalex.org/G487325141","display_name":"CBET-EPSRC: Developing standardized cell-free systems for prototyping complex synthetic biology circuits and pathways","funder_award_id":"1903477","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G582811279","display_name":null,"funder_award_id":"W911NF-19-2-0026","funder_id":"https://openalex.org/F4320338281","funder_display_name":"Army Research Office"},{"id":"https://openalex.org/G608057831","display_name":null,"funder_award_id":"W911NF-19","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7452299184","display_name":null,"funder_award_id":"W911NF","funder_id":"https://openalex.org/F4320338281","funder_display_name":"Army Research Office"},{"id":"https://openalex.org/G8376237565","display_name":null,"funder_award_id":"CBET-1903477","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8415477955","display_name":null,"funder_award_id":"W911NF-19","funder_id":"https://openalex.org/F4320338281","funder_display_name":"Army Research Office"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309398","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055"},{"id":"https://openalex.org/F4320332180","display_name":"Defense Advanced Research Projects Agency","ror":"https://ror.org/02caytj08"},{"id":"https://openalex.org/F4320332815","display_name":"Advanced Research Projects Agency","ror":"https://ror.org/02caytj08"},{"id":"https://openalex.org/F4320337390","display_name":"Division of Chemical, Bioengineering, Environmental, and Transport Systems","ror":"https://ror.org/0471zv972"},{"id":"https://openalex.org/F4320338281","display_name":"Army Research Office","ror":"https://ror.org/05epdh915"},{"id":"https://openalex.org/F4320338502","display_name":"Institute for Collaborative Biotechnologies","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":66,"referenced_works":["https://openalex.org/W1547592345","https://openalex.org/W1645305843","https://openalex.org/W1971548821","https://openalex.org/W1995035373","https://openalex.org/W2000804241","https://openalex.org/W2008591003","https://openalex.org/W2015247905","https://openalex.org/W2028695285","https://openalex.org/W2034375827","https://openalex.org/W2050630660","https://openalex.org/W2060184615","https://openalex.org/W2075031385","https://openalex.org/W2075760625","https://openalex.org/W2077300851","https://openalex.org/W2094831175","https://openalex.org/W2097240335","https://openalex.org/W2098367419","https://openalex.org/W2102653059","https://openalex.org/W2107062718","https://openalex.org/W2115740561","https://openalex.org/W2125615370","https://openalex.org/W2134759932","https://openalex.org/W2150908245","https://openalex.org/W2158055296","https://openalex.org/W2167154952","https://openalex.org/W2169360734","https://openalex.org/W2303100661","https://openalex.org/W2313697469","https://openalex.org/W2316378629","https://openalex.org/W2330245166","https://openalex.org/W2397519005","https://openalex.org/W2441893520","https://openalex.org/W2528271650","https://openalex.org/W2535730799","https://openalex.org/W2747253451","https://openalex.org/W2782104605","https://openalex.org/W2800282183","https://openalex.org/W2803345807","https://openalex.org/W2810755205","https://openalex.org/W2884300959","https://openalex.org/W2888658056","https://openalex.org/W2889406612","https://openalex.org/W2898671507","https://openalex.org/W2899225483","https://openalex.org/W2900498998","https://openalex.org/W2915371811","https://openalex.org/W2945009859","https://openalex.org/W2951120117","https://openalex.org/W2952620388","https://openalex.org/W2962763722","https://openalex.org/W3006113212","https://openalex.org/W3034583983","https://openalex.org/W3041125761","https://openalex.org/W3104222895","https://openalex.org/W3105042967","https://openalex.org/W3128508767","https://openalex.org/W3155980456","https://openalex.org/W3159193180","https://openalex.org/W3214395221","https://openalex.org/W4210560508","https://openalex.org/W4211125927","https://openalex.org/W4238640588","https://openalex.org/W4241685680","https://openalex.org/W4300672336","https://openalex.org/W4323662956","https://openalex.org/W6747644443"],"related_works":["https://openalex.org/W2150908245","https://openalex.org/W2211443823","https://openalex.org/W2043776573","https://openalex.org/W3091139413","https://openalex.org/W2152827261","https://openalex.org/W2057769265","https://openalex.org/W2367709763","https://openalex.org/W2735157934","https://openalex.org/W2097410126","https://openalex.org/W2115343689"],"abstract_inverted_index":{"Biochemical":[0],"interactions":[1],"in":[2,39,145],"systems":[3],"and":[4,55,76,99,126,144,188,198],"synthetic":[5],"biology":[6],"are":[7],"often":[8,120],"modeled":[9],"with":[10,85,108],"chemical":[11],"reaction":[12],"networks":[13],"(CRNs).":[14],"CRNs":[15],"provide":[16],"a":[17,24,35,48,89,153],"principled":[18],"modeling":[19,199],"environment":[20],"capable":[21],"of":[22,27,51,69,91,101],"expressing":[23],"huge":[25],"range":[26],"biochemical":[28,52,93,102,191,195],"processes.":[29],"In":[30],"this":[31],"paper,":[32],"we":[33],"present":[34],"software":[36,150],"toolbox,":[37],"written":[38],"Python,":[40],"that":[41],"compiles":[42],"high-level":[43,124,130],"design":[44,109,131],"specifications":[45],"represented":[46,106],"using":[47,164,174,193],"modular":[49,92],"library":[50,90],"parts,":[53],"mechanisms,":[54],"contexts":[56],"to":[57,104,159,181],"CRN":[58,72,115],"implementations.":[59],"This":[60,117],"compilation":[61],"process":[62],"offers":[63],"four":[64],"advantages.":[65],"First,":[66],"the":[67,70,113,119],"building":[68],"actual":[71],"representation":[73],"is":[74],"automatic":[75],"outputs":[77],"Systems":[78],"Biology":[79],"Markup":[80],"Language":[81],"(SBML)":[82],"models":[83,163,192],"compatible":[84],"numerous":[86],"simulators.":[87],"Second,":[88],"components":[94],"allows":[95,157],"for":[96],"different":[97],"architectures":[98],"implementations":[100],"circuits":[103],"be":[105,134,170],"succinctly":[107],"choices":[110],"propagated":[111],"throughout":[112],"underlying":[114],"automatically.":[116],"prevents":[118],"occurring":[121],"mismatch":[122],"between":[123],"designs":[125],"model":[127],"dynamics.":[128],"Third,":[129],"specification":[132],"can":[133,169,184],"embedded":[135],"into":[136],"diverse":[137,194],"biomolecular":[138],"environments,":[139,197],"such":[140],"as":[141],"cell-free":[142],"extracts":[143],"vivo":[146],"milieus.":[147],"Finally,":[148],"our":[149],"toolbox":[151],"has":[152],"parameter":[154],"database,":[155],"which":[156,168],"users":[158,176],"rapidly":[160],"prototype":[161],"large":[162],"very":[165],"few":[166],"parameters":[167],"customized":[171],"later.":[172],"By":[173],"BioCRNpyler,":[175],"ranging":[177],"from":[178],"expert":[179],"modelers":[180],"novice":[182],"script-writers":[183],"easily":[185],"build,":[186],"manage,":[187],"explore":[189],"sophisticated":[190],"implementations,":[196],"assumptions.":[200]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2017,"cited_by_count":1}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}