{"id":"https://openalex.org/W2604132648","doi":"https://doi.org/10.1186/s12859-017-1615-y","title":"The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism","display_name":"The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism","publication_year":2017,"publication_date":"2017-04-05","ids":{"openalex":"https://openalex.org/W2604132648","doi":"https://doi.org/10.1186/s12859-017-1615-y","mag":"2604132648","pmid":"https://pubmed.ncbi.nlm.nih.gov/28381205"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-017-1615-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1615-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-017-1615-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-017-1615-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016991859","display_name":"Garrett W. Birkel","orcid":null},"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/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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Garrett W. Birkel","raw_affiliation_strings":["Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","DOE Agile BioFoundry, Emeryville, CA, USA","Joint BioEnergy Institute, Emeryville, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"DOE Agile BioFoundry, Emeryville, CA, USA","institution_ids":[]},{"raw_affiliation_string":"Joint BioEnergy Institute, Emeryville, CA, USA","institution_ids":["https://openalex.org/I53012624"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039187573","display_name":"Amit Ghosh","orcid":"https://orcid.org/0000-0003-3514-885X"},"institutions":[{"id":"https://openalex.org/I145894827","display_name":"Indian Institute of Technology Kharagpur","ror":"https://ror.org/03w5sq511","country_code":"IN","type":"education","lineage":["https://openalex.org/I145894827"]},{"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/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"]}],"countries":["IN","US"],"is_corresponding":false,"raw_author_name":"Amit Ghosh","raw_affiliation_strings":["Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","Joint BioEnergy Institute, Emeryville, CA, USA","School of Energy Science and Engineering, Indian Institute of Technology (IIT), Kharagpur, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Joint BioEnergy Institute, Emeryville, CA, USA","institution_ids":["https://openalex.org/I53012624"]},{"raw_affiliation_string":"School of Energy Science and Engineering, Indian Institute of Technology (IIT), Kharagpur, India","institution_ids":["https://openalex.org/I145894827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100460647","display_name":"Vinay Kumar","orcid":"https://orcid.org/0000-0003-0077-0956"},"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/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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vinay S. Kumar","raw_affiliation_strings":["Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","Joint BioEnergy Institute, Emeryville, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Joint BioEnergy Institute, Emeryville, CA, USA","institution_ids":["https://openalex.org/I53012624"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091668355","display_name":"Daniel Weaver","orcid":"https://orcid.org/0000-0002-2906-3019"},"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/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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel Weaver","raw_affiliation_strings":["Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","Joint BioEnergy Institute, Emeryville, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Joint BioEnergy Institute, Emeryville, CA, USA","institution_ids":["https://openalex.org/I53012624"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000005456","display_name":"David Ando","orcid":null},"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/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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David Ando","raw_affiliation_strings":["Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","Joint BioEnergy Institute, Emeryville, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Joint BioEnergy Institute, Emeryville, CA, USA","institution_ids":["https://openalex.org/I53012624"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031739103","display_name":"Tyler W. H. Backman","orcid":"https://orcid.org/0000-0002-6056-353X"},"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/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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tyler W. H. Backman","raw_affiliation_strings":["Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","DOE Agile BioFoundry, Emeryville, CA, USA","Joint BioEnergy Institute, Emeryville, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"DOE Agile BioFoundry, Emeryville, CA, USA","institution_ids":[]},{"raw_affiliation_string":"Joint BioEnergy Institute, Emeryville, CA, USA","institution_ids":["https://openalex.org/I53012624"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066623854","display_name":"Adam P. Arkin","orcid":"https://orcid.org/0000-0002-4999-2931"},"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/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adam P. Arkin","raw_affiliation_strings":["Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","Department of Bioengineering, University of California, Berkeley, CA, USA","Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Department of Bioengineering, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","institution_ids":["https://openalex.org/I148283060"]}]},{"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/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"]}],"countries":["DK","US"],"is_corresponding":false,"raw_author_name":"Jay D. Keasling","raw_affiliation_strings":["Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","Department of Bioengineering, University of California, Berkeley, CA, USA","Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA","Joint BioEnergy Institute, Emeryville, CA, USA","Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, H\u00f8rsholm, DK2970, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Department of Bioengineering, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Joint BioEnergy Institute, Emeryville, CA, USA","institution_ids":["https://openalex.org/I53012624"]},{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, H\u00f8rsholm, DK2970, Denmark","institution_ids":["https://openalex.org/I2801134892"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003905928","display_name":"H\u00e9ctor Garc\u00eda Mart\u00edn","orcid":"https://orcid.org/0000-0002-4556-9685"},"institutions":[{"id":"https://openalex.org/I138285227","display_name":"Agilent Technologies (United States)","ror":"https://ror.org/02tryst02","country_code":"US","type":"company","lineage":["https://openalex.org/I138285227"]},{"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/I2802176441","display_name":"Basque Center for Applied Mathematics","ror":"https://ror.org/03b21sh32","country_code":"ES","type":"education","lineage":["https://openalex.org/I2802176441"]},{"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"]}],"countries":["ES","US"],"is_corresponding":true,"raw_author_name":"H\u00e9ctor Garc\u00eda Mart\u00edn","raw_affiliation_strings":["BCAM, Basque Center for Applied Mathematics, Bilbao, Spain. hgmartin@lbl.gov","Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. hgmartin@lbl.gov","DOE Agile BioFoundry, Emeryville, CA, USA. hgmartin@lbl.gov","Joint BioEnergy Institute, Emeryville, CA, USA. hgmartin@lbl.gov","Joint BioEnergy Institute, Emeryville, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-4556-9685","affiliations":[{"raw_affiliation_string":"BCAM, Basque Center for Applied Mathematics, Bilbao, Spain. hgmartin@lbl.gov","institution_ids":["https://openalex.org/I2802176441"]},{"raw_affiliation_string":"Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. hgmartin@lbl.gov","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"DOE Agile BioFoundry, Emeryville, CA, USA. hgmartin@lbl.gov","institution_ids":["https://openalex.org/I138285227"]},{"raw_affiliation_string":"Joint BioEnergy Institute, Emeryville, CA, USA. hgmartin@lbl.gov","institution_ids":["https://openalex.org/I53012624"]},{"raw_affiliation_string":"Joint BioEnergy Institute, Emeryville, CA, USA","institution_ids":["https://openalex.org/I53012624"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5003905928"],"corresponding_institution_ids":["https://openalex.org/I138285227","https://openalex.org/I148283060","https://openalex.org/I2802176441","https://openalex.org/I53012624"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":1.5531,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.82561943,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"18","issue":"1","first_page":"205","last_page":"205"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9904000163078308,"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":0.9904000163078308,"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/T12688","display_name":"Microbial metabolism and enzyme function","score":0.002099999925121665,"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/T10631","display_name":"Cancer, Hypoxia, and Metabolism","score":0.0007999999797903001,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/python","display_name":"Python (programming language)","score":0.6569551229476929},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44408583641052246},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4395511746406555},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3512052297592163},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3351179361343384},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2846960425376892},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1570945382118225}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6569551229476929},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44408583641052246},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4395511746406555},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3512052297592163},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3351179361343384},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2846960425376892},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1570945382118225}],"mesh":[{"descriptor_ui":"D002247","descriptor_name":"Carbon Isotopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002247","descriptor_name":"Carbon Isotopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002247","descriptor_name":"Carbon Isotopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056804","descriptor_name":"Biofuels","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056804","descriptor_name":"Biofuels","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056804","descriptor_name":"Biofuels","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064688","descriptor_name":"Metabolic Flux Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064688","descriptor_name":"Metabolic Flux Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064688","descriptor_name":"Metabolic Flux Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":11,"locations":[{"id":"doi:10.1186/s12859-017-1615-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1615-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-017-1615-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28381205","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28381205","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":"BMC bioinformatics","raw_type":"Journal Article"},{"id":"pmid:28420344","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28420344","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":"BMC bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:bird.bcamath.org:20.500.11824/661","is_oa":false,"landing_page_url":"http://hdl.handle.net/20.500.11824/661","pdf_url":null,"source":{"id":"https://openalex.org/S4306401608","display_name":"BIRD (Basque Center for Applied Mathematics)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2802176441","host_organization_name":"Basque Center for Applied Mathematics","host_organization_lineage":["https://openalex.org/I2802176441"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5382524","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5382524","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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:ark:/13030/qt9mq1k5p3","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:97efd12eba8047718e7bf3427294a120","is_oa":false,"landing_page_url":"https://doaj.org/article/97efd12eba8047718e7bf3427294a120","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":"BMC Bioinformatics, Vol 18, Iss 1, Pp 1-11 (2017)","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt9mq1k5p3","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/9mq1k5p3","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC bioinformatics, vol 18, iss 1","raw_type":"article"},{"id":"pmh:oai:osti.gov:1379799","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1379799","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:osti.gov:1618524","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1618524","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:qt9mq1k5p3","is_oa":false,"landing_page_url":"http://www.escholarship.org/uc/item/9mq1k5p3","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Birkel, GW; Ghosh, A; Kumar, VS; Weaver, D; Ando, D; Backman, TWH; \u00c2\u00a0et al.(2017). The JBEI quantitative metabolic modeling library (jQMM): A python library for modeling microbial metabolism. BMC Bioinformatics, 18(1). doi: 10.1186/s12859-017-1615-y. UC Berkeley: Retrieved from: http://www.escholarship.org/uc/item/9mq1k5p3","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-017-1615-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1615-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-017-1615-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1079818582","display_name":null,"funder_award_id":"AC02\u201005CH11231","funder_id":"https://openalex.org/F4320338292","funder_display_name":"Lawrence Berkeley National Laboratory"},{"id":"https://openalex.org/G1143651532","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320338292","funder_display_name":"Lawrence Berkeley National Laboratory"},{"id":"https://openalex.org/G1286236842","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G1337544421","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G1708820433","display_name":null,"funder_award_id":"BERC 2014-2017 program","funder_id":"https://openalex.org/F4320321705","funder_display_name":"Eusko Jaurlaritza"},{"id":"https://openalex.org/G223002938","display_name":null,"funder_award_id":"DE-AC02 \u2212 05CH11231","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G3083819904","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G3244436707","display_name":null,"funder_award_id":"SEV-2013-0323","funder_id":"https://openalex.org/F4320328444","funder_display_name":"Basque Center for Applied Mathematics"},{"id":"https://openalex.org/G3779338858","display_name":null,"funder_award_id":"2014-2017","funder_id":"https://openalex.org/F4320321705","funder_display_name":"Eusko Jaurlaritza"},{"id":"https://openalex.org/G419881185","display_name":null,"funder_award_id":"DEAC02\u201305CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4252991836","display_name":null,"funder_award_id":"BERC 2014-2017","funder_id":"https://openalex.org/F4320321837","funder_display_name":"Ministerio de Econom\u00eda y Competitividad"},{"id":"https://openalex.org/G42916606","display_name":null,"funder_award_id":"DE AC02 05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G4373130462","display_name":null,"funder_award_id":"2013-0323","funder_id":"https://openalex.org/F4320321837","funder_display_name":"Ministerio de Econom\u00eda y Competitividad"},{"id":"https://openalex.org/G4501827968","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4893884145","display_name":null,"funder_award_id":"DE AC02-05CH11231","funder_id":"https://openalex.org/F4320321837","funder_display_name":"Ministerio de Econom\u00eda y Competitividad"},{"id":"https://openalex.org/G498139845","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G5281057304","display_name":null,"funder_award_id":"2014-2017","funder_id":"https://openalex.org/F4320321837","funder_display_name":"Ministerio de Econom\u00eda y Competitividad"},{"id":"https://openalex.org/G6652958823","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G711474080","display_name":null,"funder_award_id":"BERC (2014\u20132017)","funder_id":"https://openalex.org/F4320321705","funder_display_name":"Eusko Jaurlaritza"},{"id":"https://openalex.org/G7354628648","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320338292","funder_display_name":"Lawrence Berkeley National Laboratory"},{"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/G7787287669","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G8296132195","display_name":null,"funder_award_id":"SEV-2013-0323","funder_id":"https://openalex.org/F4320321705","funder_display_name":"Eusko Jaurlaritza"},{"id":"https://openalex.org/G862438431","display_name":null,"funder_award_id":"SEV\u20102013\u20100323","funder_id":"https://openalex.org/F4320321837","funder_display_name":"Ministerio de Econom\u00eda y Competitividad"},{"id":"https://openalex.org/G969889393","display_name":null,"funder_award_id":"DE-AC02-","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320321705","display_name":"Eusko Jaurlaritza","ror":"https://ror.org/00pz2fp31"},{"id":"https://openalex.org/F4320321837","display_name":"Ministerio de Econom\u00eda y Competitividad","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"},{"id":"https://openalex.org/F4320328444","display_name":"Basque Center for Applied Mathematics","ror":"https://ror.org/03b21sh32"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"},{"id":"https://openalex.org/F4320337509","display_name":"Biological and Environmental Research","ror":"https://ror.org/0114b2m14"},{"id":"https://openalex.org/F4320338292","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2604132648.pdf","grobid_xml":"https://content.openalex.org/works/W2604132648.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1830293097","https://openalex.org/W1911715606","https://openalex.org/W1981100467","https://openalex.org/W1982291387","https://openalex.org/W1990994166","https://openalex.org/W1992170087","https://openalex.org/W1996588166","https://openalex.org/W2006672203","https://openalex.org/W2008421457","https://openalex.org/W2014323212","https://openalex.org/W2016652826","https://openalex.org/W2019962216","https://openalex.org/W2021654871","https://openalex.org/W2022828569","https://openalex.org/W2024130925","https://openalex.org/W2025363287","https://openalex.org/W2048465561","https://openalex.org/W2052386819","https://openalex.org/W2061939373","https://openalex.org/W2074044468","https://openalex.org/W2078546696","https://openalex.org/W2082382448","https://openalex.org/W2089632603","https://openalex.org/W2094714976","https://openalex.org/W2096245011","https://openalex.org/W2096642289","https://openalex.org/W2097020868","https://openalex.org/W2100398170","https://openalex.org/W2102164505","https://openalex.org/W2107292394","https://openalex.org/W2111943920","https://openalex.org/W2119683611","https://openalex.org/W2127636197","https://openalex.org/W2131966673","https://openalex.org/W2134138595","https://openalex.org/W2146095405","https://openalex.org/W2147472054","https://openalex.org/W2154767435","https://openalex.org/W2158287690","https://openalex.org/W2158688625","https://openalex.org/W2160252043","https://openalex.org/W2293809279","https://openalex.org/W2328214874","https://openalex.org/W2761518648","https://openalex.org/W4238101851","https://openalex.org/W7067216465"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W1699080303","https://openalex.org/W4297799326","https://openalex.org/W3116064965","https://openalex.org/W4287027380"],"abstract_inverted_index":{"Modeling":[0],"of":[1,7,34,46,53,60,88,130,148,202,220,229,258,269,298],"microbial":[2],"metabolism":[3,132,271],"is":[4,59,224],"a":[5,16,139,182,200,203],"topic":[6],"growing":[8],"importance":[9],"in":[10,56],"biotechnology.":[11],"Mathematical":[12],"modeling":[13,42,117],"helps":[14],"provide":[15,239],"mechanistic":[17],"understanding":[18],"for":[19,63,84,116,126,142,260],"the":[20,24,28,32,44,51,75,85,89,127,167,197,218,221,227,240,246,253,289,294],"studied":[21],"process,":[22],"separating":[23],"main":[25],"drivers":[26],"from":[27,288],"circumstantial":[29],"ones,":[30],"bounding":[31],"outcomes":[33],"experiments":[35],"and":[36,71,94,101,121,133,158,238,255,262,272,291],"guiding":[37],"engineering":[38,65,257],"approaches.":[39],"Among":[40],"different":[41,146],"schemes,":[43],"quantification":[45],"intracellular":[47],"metabolic":[48,64,119,256,299],"fluxes":[49,120],"(i.e.":[50,98],"rate":[52],"each":[54],"reaction":[55],"cellular":[57,131,270],"metabolism)":[58],"particular":[61],"interest":[62],"because":[66],"it":[67,137,165,284],"describes":[68],"how":[69],"carbon":[70],"energy":[72],"flow":[73],"throughout":[74],"cell.":[76],"In":[77,195],"addition":[78,228],"to":[79,169,176,209,213,242,245],"flux":[80,149],"analysis,":[81],"new":[82],"methods":[83],"effective":[86],"use":[87,170,219],"ever":[90],"more":[91],"readily":[92],"available":[93],"abundant":[95],"-omics":[96,124,274],"data":[97,125,175,208],"transcriptomics,":[99],"proteomics":[100,207],"metabolomics)":[102],"are":[103,152],"urgently":[104],"needed.":[105],"The":[106],"jQMM":[107,222,250],"library":[108,198,223],"presented":[109],"here":[110],"provides":[111],"an":[112,277],"open-source,":[113],"Python-based":[114],"framework":[115],"internal":[118],"leveraging":[122,273],"other":[123,263],"scientific":[128],"study":[129],"bioengineering":[134],"purposes.":[135],"Firstly,":[136],"presents":[138],"complete":[140],"toolbox":[141],"simultaneously":[143],"performing":[144],"two":[145],"types":[147],"analysis":[150],"that":[151,205,235],"typically":[153],"disjoint:":[154],"Flux":[155,162,189],"Balance":[156],"Analysis":[157,190],"13":[159,171,186,192],"C":[160,172,187,193],"Metabolic":[161,188],"Analysis.":[163],"Moreover,":[164],"introduces":[166],"capability":[168,241],"labeling":[173],"experimental":[174],"constrain":[177],"comprehensive":[178],"genome-scale":[179],"models":[180],"through":[181,226],"technique":[183],"called":[184],"two-scale":[185],"(2S-":[191],"MFA).":[194],"addition,":[196],"includes":[199],"demonstration":[201,233],"method":[204],"uses":[206],"produce":[210],"actionable":[211],"insights":[212],"increase":[214],"biofuel":[215],"production.":[216],"Finally,":[217],"illustrated":[225],"several":[230],"Jupyter":[231],"notebook":[232],"files":[234],"enhance":[236],"reproducibility":[237],"be":[243],"adapted":[244],"user\u2019s":[247],"specific":[248],"needs.":[249],"will":[251,285],"facilitate":[252],"design":[254],"organisms":[259],"biofuels":[261],"chemicals,":[264],"as":[265,267],"well":[266],"investigations":[268],"data.":[275],"As":[276],"open":[278],"source":[279],"software":[280],"project,":[281],"we":[282],"hope":[283],"attract":[286],"additions":[287],"community":[290],"grow":[292],"with":[293],"rapidly":[295],"changing":[296],"field":[297],"engineering.":[300]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":4}],"updated_date":"2026-09-02T18:50:13.731487","created_date":"2025-10-10T00:00:00"}
