{"id":"https://openalex.org/W4392581764","doi":"https://doi.org/10.1371/journal.pcbi.1011929","title":"teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering","display_name":"teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering","publication_year":2024,"publication_date":"2024-03-08","ids":{"openalex":"https://openalex.org/W4392581764","doi":"https://doi.org/10.1371/journal.pcbi.1011929","pmid":"https://pubmed.ncbi.nlm.nih.gov/38457467"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011929","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011929","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.1011929","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052142333","display_name":"S\u00f8ren D. Petersen","orcid":"https://orcid.org/0000-0003-4104-5144"},"institutions":[{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"S\u00f8ren D. Petersen","raw_affiliation_strings":["Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark"],"raw_orcid":"https://orcid.org/0000-0003-4104-5144","affiliations":[{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092201551","display_name":"Lucas Levassor","orcid":"https://orcid.org/0000-0002-3261-9911"},"institutions":[{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Lucas Levassor","raw_affiliation_strings":["Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark","Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark"],"raw_orcid":"https://orcid.org/0000-0002-3261-9911","affiliations":[{"raw_affiliation_string":"Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]},{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101214340","display_name":"Christine M. Pedersen","orcid":null},"institutions":[{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Christine M. Pedersen","raw_affiliation_strings":["Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056287081","display_name":"Jan Madsen","orcid":"https://orcid.org/0000-0002-5098-8454"},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Jan Madsen","raw_affiliation_strings":["Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060098890","display_name":"Lea G. Hansen","orcid":"https://orcid.org/0000-0002-8454-312X"},"institutions":[{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Lea G. Hansen","raw_affiliation_strings":["Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090330706","display_name":"Jie Zhang","orcid":"https://orcid.org/0000-0003-4119-9442"},"institutions":[{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Jie Zhang","raw_affiliation_strings":["Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076090836","display_name":"Ahmad K. Haidar","orcid":null},"institutions":[{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Ahmad K. Haidar","raw_affiliation_strings":["Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078562966","display_name":"Rasmus John Normand Frandsen","orcid":"https://orcid.org/0000-0002-3799-6062"},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Rasmus J. N. Frandsen","raw_affiliation_strings":["Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000312223","display_name":"Jay D. Keasling","orcid":"https://orcid.org/0000-0003-4170-6088"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]},{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]},{"id":"https://openalex.org/I53012624","display_name":"Joint BioEnergy Institute","ror":"https://ror.org/03ww55028","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I53012624"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["CN","DK","US"],"is_corresponding":false,"raw_author_name":"Jay D. Keasling","raw_affiliation_strings":["Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America","Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China","Department of Chemical and Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California, United States of America","Joint BioEnergy Institute, Emeryville, California, United States of America","Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China","institution_ids":["https://openalex.org/I4210145761"]},{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Joint BioEnergy Institute, Emeryville, California, United States of America","institution_ids":["https://openalex.org/I53012624"]},{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086274481","display_name":"Tilmann Weber","orcid":"https://orcid.org/0000-0002-8260-5120"},"institutions":[{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Tilmann Weber","raw_affiliation_strings":["Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003812348","display_name":"Nikolaus Sonnenschein","orcid":"https://orcid.org/0000-0002-7581-4936"},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Nikolaus Sonnenschein","raw_affiliation_strings":["Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024318421","display_name":"Michael K. Jensen","orcid":"https://orcid.org/0000-0001-7574-4707"},"institutions":[{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":true,"raw_author_name":"Michael K. Jensen","raw_affiliation_strings":["Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark"],"raw_orcid":"https://orcid.org/0000-0001-7574-4707","affiliations":[{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I96673099"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5024318421"],"corresponding_institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I96673099"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.1945,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.87860201,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"20","issue":"3","first_page":"e1011929","last_page":"e1011929"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9969000220298767,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9969000220298767,"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/T11663","display_name":"Viral Infectious Diseases and Gene Expression in Insects","score":0.9943000078201294,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9879999756813049,"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/synthetic-biology","display_name":"Synthetic biology","score":0.8107076287269592},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7230624556541443},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.629443883895874},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6085949540138245},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.5017828941345215},{"id":"https://openalex.org/keywords/application-programming-interface","display_name":"Application programming interface","score":0.49705269932746887},{"id":"https://openalex.org/keywords/reuse","display_name":"Reuse","score":0.4779358208179474},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4333460330963135},{"id":"https://openalex.org/keywords/design-cycle","display_name":"Design cycle","score":0.4286605417728424},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.29644277691841125},{"id":"https://openalex.org/keywords/systems-engineering","display_name":"Systems engineering","score":0.21096038818359375},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.18076810240745544},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.12267780303955078},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.11204800009727478},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10771122574806213},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09903162717819214}],"concepts":[{"id":"https://openalex.org/C191908910","wikidata":"https://www.wikidata.org/wiki/Q862838","display_name":"Synthetic biology","level":2,"score":0.8107076287269592},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7230624556541443},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.629443883895874},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6085949540138245},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.5017828941345215},{"id":"https://openalex.org/C99613125","wikidata":"https://www.wikidata.org/wiki/Q165194","display_name":"Application programming interface","level":2,"score":0.49705269932746887},{"id":"https://openalex.org/C206588197","wikidata":"https://www.wikidata.org/wiki/Q846574","display_name":"Reuse","level":2,"score":0.4779358208179474},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4333460330963135},{"id":"https://openalex.org/C2982740150","wikidata":"https://www.wikidata.org/wiki/Q5249230","display_name":"Design cycle","level":2,"score":0.4286605417728424},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.29644277691841125},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.21096038818359375},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.18076810240745544},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.12267780303955078},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.11204800009727478},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10771122574806213},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09903162717819214},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001698","descriptor_name":"Biomedical Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001698","descriptor_name":"Biomedical Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001698","descriptor_name":"Biomedical Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057005","descriptor_name":"Bioengineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057005","descriptor_name":"Bioengineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057005","descriptor_name":"Bioengineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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},{"descriptor_ui":"D060847","descriptor_name":"Metabolic Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060847","descriptor_name":"Metabolic Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060847","descriptor_name":"Metabolic Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1011929","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011929","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:38457467","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38457467","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:escholarship.org:ark:/13030/qt97m6t2tv","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/97m6t2tv","pdf_url":"https://escholarship.org/content/qt97m6t2tv/qt97m6t2tv.pdf?t=sb3u33","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLOS Computational Biology, vol 20, iss 3","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10954146","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10954146","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10954146/pdf/pcbi.1011929.pdf","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"},{"id":"pmh:oai:doaj.org/article:c2a8272c0f8f4e8583e467f28cf7f764","is_oa":false,"landing_page_url":"https://doaj.org/article/c2a8272c0f8f4e8583e467f28cf7f764","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"PLoS Computational Biology, Vol 20, Iss 3, p e1011929 (2024)","raw_type":"article"},{"id":"pmh:oai:osti.gov:2470853","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/2470853","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:pure.atira.dk:publications/9eeb7301-8b74-489a-87d6-ce3b77a7f3cd","is_oa":true,"landing_page_url":"https://orbit.dtu.dk/en/publications/9eeb7301-8b74-489a-87d6-ce3b77a7f3cd","pdf_url":null,"source":{"id":"https://openalex.org/S4306400705","display_name":"Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I96673099","host_organization_name":"Technical University of Denmark","host_organization_lineage":["https://openalex.org/I96673099"],"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":"Petersen , S D , Levassor , L , Pedersen , C M , Madsen , J , Hansen , L G , Zhang , J , Haidar , A K , Frandsen , R J N , Keasling , J D , Weber , T , Sonnenschein , N & K. Jensen , M 2024 , ' teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering ' , PLOS Computational Biology , vol. 20 , no. 3 , e1011929 . https://doi.org/10.1371/journal.pcbi.1011929","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011929","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011929","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":[{"score":0.5600000023841858,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G4674521716","display_name":null,"funder_award_id":"NNF17SA0031362","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"},{"id":"https://openalex.org/G7042228497","display_name":null,"funder_award_id":"NNF20CC0035580","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"},{"id":"https://openalex.org/G7701966108","display_name":null,"funder_award_id":"NNF10CC1016517","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"},{"id":"https://openalex.org/G8175829662","display_name":null,"funder_award_id":"814645","funder_id":"https://openalex.org/F4320338335","funder_display_name":"H2020 European Research Council"}],"funders":[{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"},{"id":"https://openalex.org/F4320338335","display_name":"H2020 European Research Council","ror":"https://ror.org/0472cxd90"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":50,"referenced_works":["https://openalex.org/W1555560879","https://openalex.org/W1972254777","https://openalex.org/W1994896760","https://openalex.org/W2011945340","https://openalex.org/W2036910166","https://openalex.org/W2040834897","https://openalex.org/W2078934089","https://openalex.org/W2096525273","https://openalex.org/W2104619491","https://openalex.org/W2140158011","https://openalex.org/W2143913679","https://openalex.org/W2161645265","https://openalex.org/W2167550136","https://openalex.org/W2293809279","https://openalex.org/W2302501749","https://openalex.org/W2753048940","https://openalex.org/W2790018487","https://openalex.org/W2895347486","https://openalex.org/W2911320144","https://openalex.org/W2912316140","https://openalex.org/W2914462572","https://openalex.org/W2943995236","https://openalex.org/W2949078105","https://openalex.org/W2950954328","https://openalex.org/W2952157594","https://openalex.org/W2963285572","https://openalex.org/W2963907999","https://openalex.org/W2981792167","https://openalex.org/W3029928583","https://openalex.org/W3068311477","https://openalex.org/W3082772719","https://openalex.org/W3088063380","https://openalex.org/W3093164423","https://openalex.org/W3111667196","https://openalex.org/W3126838605","https://openalex.org/W3159193120","https://openalex.org/W3163739989","https://openalex.org/W3209916183","https://openalex.org/W3211655359","https://openalex.org/W4205228445","https://openalex.org/W4205440119","https://openalex.org/W4242395378","https://openalex.org/W4284685541","https://openalex.org/W4289274885","https://openalex.org/W4293503763","https://openalex.org/W4293792996","https://openalex.org/W4313880130","https://openalex.org/W4320004594","https://openalex.org/W4382985378","https://openalex.org/W4386116890"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W2093262417","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W1699080303","https://openalex.org/W4312626803","https://openalex.org/W4297799326","https://openalex.org/W3116064965","https://openalex.org/W2123131699","https://openalex.org/W4287027380"],"abstract_inverted_index":{"Synthetic":[0],"biology":[1,16,47],"dictates":[2],"the":[3,18,51,57,71,83,96],"data-driven":[4],"engineering":[5,86,97,155],"of":[6,32,70,98,156,162],"biocatalysis,":[7],"cellular":[8],"functions,":[9],"and":[10,25,34,40,54,63,74,93,108,125,141,146,150,179],"organism":[11],"behavior.":[12],"Integral":[13],"to":[14,20,79,166],"synthetic":[15],"is":[17,48,122,126,174],"aspiration":[19],"efficiently":[21],"find,":[22],"access,":[23],"interoperate,":[24],"reuse":[26],"high-quality":[27],"data":[28,65],"on":[29,118],"genotype-phenotype":[30],"relationships":[31],"native":[33],"engineered":[35],"biosystems":[36],"under":[37,112],"FAIR":[38,130],"principles,":[39],"from":[41],"this":[42,133],"facilitate":[43],"forward-engineering":[44],"strategies.":[45],"However,":[46],"complex":[49],"at":[50,56,67,177],"regulatory":[52],"level,":[53,59],"noisy":[55],"operational":[58],"thus":[60],"necessitating":[61],"systematic":[62],"diligent":[64],"handling":[66],"all":[68],"levels":[69],"design,":[72],"build,":[73],"test":[75],"phases":[76],"in":[77,82,169],"order":[78],"maximize":[80],"learning":[81],"iterative":[84],"design-build-test-learn":[85],"cycle.":[87],"To":[88],"enable":[89],"user-friendly":[90],"simulation,":[91],"organization,":[92],"guidance":[94],"for":[95,138,153,160],"biosystems,":[99],"we":[100,135],"have":[101],"developed":[102],"an":[103],"open-source":[104],"python-based":[105],"computer-aided":[106],"design":[107],"analysis":[109],"platform":[110,121,173],"operating":[111],"a":[113,163],"literate":[114],"programming":[115],"user-interface":[116],"hosted":[117],"Github.":[119],"The":[120,171],"called":[123],"teemi":[124,137,172],"fully":[127],"compliant":[128],"with":[129],"principles.":[131],"In":[132],"study":[134],"apply":[136],"i)":[139],"designing":[140],"simulating":[142],"bioengineering,":[143],"ii)":[144],"integrating":[145],"analyzing":[147],"multivariate":[148],"datasets,":[149],"iii)":[151],"machine-learning":[152],"predictive":[154],"metabolic":[157],"pathway":[158],"designs":[159],"production":[161],"key":[164],"precursor":[165],"medicinal":[167],"alkaloids":[168],"yeast.":[170],"publicly":[175],"available":[176],"PyPi":[178],"GitHub.":[180]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":4}],"updated_date":"2026-08-18T07:49:30.821534","created_date":"2025-10-10T00:00:00"}