{"id":"https://openalex.org/W4385801921","doi":"https://doi.org/10.1371/journal.pcbi.1011363","title":"A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia","display_name":"A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia","publication_year":2023,"publication_date":"2023-08-14","ids":{"openalex":"https://openalex.org/W4385801921","doi":"https://doi.org/10.1371/journal.pcbi.1011363","pmid":"https://pubmed.ncbi.nlm.nih.gov/37578975"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011363","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011363","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.1011363","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074450770","display_name":"William T. Scott","orcid":"https://orcid.org/0000-0002-4029-2998"},"institutions":[{"id":"https://openalex.org/I913481162","display_name":"Wageningen University & Research","ror":"https://ror.org/04qw24q55","country_code":"NL","type":"education","lineage":["https://openalex.org/I913481162"]},{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"William T. Scott","raw_affiliation_strings":["Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands","UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen, the Netherlands"],"affiliations":[{"raw_affiliation_string":"Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands","institution_ids":["https://openalex.org/I913481162"]},{"raw_affiliation_string":"UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen, the Netherlands","institution_ids":["https://openalex.org/I913481162","https://openalex.org/I98358874"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044274138","display_name":"Sara Benito-Vaquerizo","orcid":"https://orcid.org/0000-0003-3936-9676"},"institutions":[{"id":"https://openalex.org/I913481162","display_name":"Wageningen University & Research","ror":"https://ror.org/04qw24q55","country_code":"NL","type":"education","lineage":["https://openalex.org/I913481162"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Sara Benito-Vaquerizo","raw_affiliation_strings":["Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands"],"affiliations":[{"raw_affiliation_string":"Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands","institution_ids":["https://openalex.org/I913481162"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064413068","display_name":"Johannes Zimmermann","orcid":"https://orcid.org/0000-0002-5041-1954"},"institutions":[{"id":"https://openalex.org/I32021983","display_name":"Christian-Albrechts-Universit\u00e4t zu Kiel","ror":"https://ror.org/04v76ef78","country_code":"DE","type":"education","lineage":["https://openalex.org/I32021983"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Johannes Zimmermann","raw_affiliation_strings":["Christian-Albrechts-University Kiel, Institute of Experimental Medicine, Research Group Medical Systems Biology, Kiel, Germany"],"affiliations":[{"raw_affiliation_string":"Christian-Albrechts-University Kiel, Institute of Experimental Medicine, Research Group Medical Systems Biology, Kiel, Germany","institution_ids":["https://openalex.org/I32021983"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067714445","display_name":"Djordje Baji\u0107","orcid":"https://orcid.org/0000-0002-6716-7898"},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Djordje Baji\u0107","raw_affiliation_strings":["Department of Biotechnology, Delft University of Technology, Delft, the Netherlands"],"affiliations":[{"raw_affiliation_string":"Department of Biotechnology, Delft University of Technology, Delft, the Netherlands","institution_ids":["https://openalex.org/I98358874"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074416067","display_name":"Almut Heinken","orcid":"https://orcid.org/0000-0001-6938-8072"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I4387152275","display_name":"Nutrition-G\u00e9n\u00e9tique et Exposition aux Risques Environnementaux","ror":"https://ror.org/053d03003","country_code":null,"type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I4387152275","https://openalex.org/I90183372"]},{"id":"https://openalex.org/I90183372","display_name":"Universit\u00e9 de Lorraine","ror":"https://ror.org/04vfs2w97","country_code":"FR","type":"education","lineage":["https://openalex.org/I90183372"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Almut Heinken","raw_affiliation_strings":["Inserm U1256 Laboratoire nGERE, Universit\u00e9 de Lorraine, Nancy, France"],"affiliations":[{"raw_affiliation_string":"Inserm U1256 Laboratoire nGERE, Universit\u00e9 de Lorraine, Nancy, France","institution_ids":["https://openalex.org/I90183372","https://openalex.org/I4387152275","https://openalex.org/I154526488"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041170743","display_name":"Mar\u00eda Su\u00e1rez\u2010Diez","orcid":"https://orcid.org/0000-0001-5845-146X"},"institutions":[{"id":"https://openalex.org/I913481162","display_name":"Wageningen University & Research","ror":"https://ror.org/04qw24q55","country_code":"NL","type":"education","lineage":["https://openalex.org/I913481162"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Maria Suarez-Diez","raw_affiliation_strings":["Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands"],"affiliations":[{"raw_affiliation_string":"Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands","institution_ids":["https://openalex.org/I913481162"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073898339","display_name":"Peter J. Schaap","orcid":"https://orcid.org/0000-0002-4346-6084"},"institutions":[{"id":"https://openalex.org/I913481162","display_name":"Wageningen University & Research","ror":"https://ror.org/04qw24q55","country_code":"NL","type":"education","lineage":["https://openalex.org/I913481162"]},{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Peter J. Schaap","raw_affiliation_strings":["Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands","UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen, the Netherlands"],"affiliations":[{"raw_affiliation_string":"Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands","institution_ids":["https://openalex.org/I913481162"]},{"raw_affiliation_string":"UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen, the Netherlands","institution_ids":["https://openalex.org/I913481162","https://openalex.org/I98358874"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5041170743","https://openalex.org/A5044274138","https://openalex.org/A5064413068","https://openalex.org/A5067714445","https://openalex.org/A5073898339","https://openalex.org/A5074416067","https://openalex.org/A5074450770"],"corresponding_institution_ids":["https://openalex.org/I154526488","https://openalex.org/I32021983","https://openalex.org/I4387152275","https://openalex.org/I90183372","https://openalex.org/I913481162","https://openalex.org/I98358874"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":6.3031,"has_fulltext":true,"cited_by_count":38,"citation_normalized_percentile":{"value":0.97161154,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"19","issue":"8","first_page":"e1011363","last_page":"e1011363"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":1.0,"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":1.0,"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/T10171","display_name":"Biofuel production and bioconversion","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9779999852180481,"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/interoperability","display_name":"Interoperability","score":0.6232095956802368},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6030420660972595},{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.47404786944389343},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.45099425315856934},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.4262691140174866},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3801075220108032},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3479212820529938},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.2018434703350067},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.1268494725227356}],"concepts":[{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.6232095956802368},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6030420660972595},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.47404786944389343},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.45099425315856934},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.4262691140174866},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3801075220108032},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3479212820529938},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.2018434703350067},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.1268494725227356},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"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":"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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059013","descriptor_name":"Microbial Consortia","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059013","descriptor_name":"Microbial Consortia","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059013","descriptor_name":"Microbial Consortia","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1011363","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011363","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:37578975","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37578975","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:library.wur.nl:wurpubs/620851","is_oa":true,"landing_page_url":"https://research.wur.nl/en/publications/a-structured-evaluation-of-genome-scale-constraint-based-modeling-2","pdf_url":"https://edepot.wur.nl/641571","source":{"id":"https://openalex.org/S4210201231","display_name":"Socio-Environmental Systems Modeling","issn_l":"2663-3027","issn":["2663-3027"],"is_oa":true,"is_in_doaj":false,"is_core":true,"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":"ISSN: 1553-734X","raw_type":"Article/Letter to editor"},{"id":"pmh:oai:pubmedcentral.nih.gov:10449394","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10449394","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10449394/pdf/pcbi.1011363.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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:bea255732a834a03bb544b2ca97e6d86","is_oa":true,"landing_page_url":"https://doaj.org/article/bea255732a834a03bb544b2ca97e6d86","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 19, Iss 8, p e1011363 (2023)","raw_type":"article"},{"id":"pmh:oai:tudelft.nl:uuid:fd08074c-0aea-4d29-ba31-2a2e2ca35097","is_oa":true,"landing_page_url":"http://resolver.tudelft.nl/uuid:fd08074c-0aea-4d29-ba31-2a2e2ca35097","pdf_url":null,"source":{"id":"https://openalex.org/S4306400906","display_name":"Research Repository (Delft University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98358874","host_organization_name":"Delft University of Technology","host_organization_lineage":["https://openalex.org/I98358874"],"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":"journal article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011363","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011363","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/G1332741550","display_name":null,"funder_award_id":"ALWGK.2016.029","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G1399324874","display_name":null,"funder_award_id":"024.002.00","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G1433606067","display_name":null,"funder_award_id":"024.002.002","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G343595216","display_name":null,"funder_award_id":"024.002.002","funder_id":"https://openalex.org/F4320321799","funder_display_name":"Ministerie van Onderwijs, Cultuur en Wetenschap"},{"id":"https://openalex.org/G5023269647","display_name":null,"funder_award_id":"2016.029","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G5365867299","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G629491556","display_name":null,"funder_award_id":"(NWO)","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G7717650332","display_name":null,"funder_award_id":"184.035.007","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"}],"funders":[{"id":"https://openalex.org/F4320309636","display_name":"University of Minnesota","ror":"https://ror.org/03grvy078"},{"id":"https://openalex.org/F4320310419","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231"},{"id":"https://openalex.org/F4320312726","display_name":"University of Oregon","ror":"https://ror.org/0293rh119"},{"id":"https://openalex.org/F4320321799","display_name":"Ministerie van Onderwijs, Cultuur en Wetenschap","ror":"https://ror.org/02x3w5g21"},{"id":"https://openalex.org/F4320321800","display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","ror":"https://ror.org/04jsz6e67"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334952","display_name":"Wageningen University and Research","ror":"https://ror.org/04qw24q55"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":110,"referenced_works":["https://openalex.org/W1135359322","https://openalex.org/W1966497610","https://openalex.org/W1974662378","https://openalex.org/W1982013068","https://openalex.org/W1984445372","https://openalex.org/W2009282793","https://openalex.org/W2014294355","https://openalex.org/W2018994057","https://openalex.org/W2028985317","https://openalex.org/W2031081192","https://openalex.org/W2031663630","https://openalex.org/W2048214825","https://openalex.org/W2048465561","https://openalex.org/W2048596643","https://openalex.org/W2074191684","https://openalex.org/W2078355959","https://openalex.org/W2096245011","https://openalex.org/W2102681753","https://openalex.org/W2108656223","https://openalex.org/W2111381495","https://openalex.org/W2111421616","https://openalex.org/W2122093325","https://openalex.org/W2123966372","https://openalex.org/W2124737787","https://openalex.org/W2127020923","https://openalex.org/W2130364940","https://openalex.org/W2136004458","https://openalex.org/W2139887779","https://openalex.org/W2146862079","https://openalex.org/W2169527381","https://openalex.org/W2169913476","https://openalex.org/W2202347610","https://openalex.org/W2207096656","https://openalex.org/W2207696866","https://openalex.org/W2264725561","https://openalex.org/W2290703973","https://openalex.org/W2295190630","https://openalex.org/W2302501749","https://openalex.org/W2316195511","https://openalex.org/W2346165860","https://openalex.org/W2551372307","https://openalex.org/W2563041887","https://openalex.org/W2564018102","https://openalex.org/W2607044251","https://openalex.org/W2616621860","https://openalex.org/W2617261748","https://openalex.org/W2762019694","https://openalex.org/W2788354600","https://openalex.org/W2809329346","https://openalex.org/W2889656931","https://openalex.org/W2890142464","https://openalex.org/W2899303334","https://openalex.org/W2913553075","https://openalex.org/W2914170023","https://openalex.org/W2928984843","https://openalex.org/W2941440692","https://openalex.org/W2950751688","https://openalex.org/W2951327715","https://openalex.org/W2952117162","https://openalex.org/W2952708805","https://openalex.org/W2952948582","https://openalex.org/W2954847673","https://openalex.org/W2966440819","https://openalex.org/W2967843340","https://openalex.org/W2977332526","https://openalex.org/W2983330093","https://openalex.org/W2990481789","https://openalex.org/W3002175424","https://openalex.org/W3010629926","https://openalex.org/W3028922180","https://openalex.org/W3035029383","https://openalex.org/W3080133182","https://openalex.org/W3087971117","https://openalex.org/W3089357338","https://openalex.org/W3094333108","https://openalex.org/W3108937084","https://openalex.org/W3109167930","https://openalex.org/W3110741547","https://openalex.org/W3118040522","https://openalex.org/W3119703439","https://openalex.org/W3128332967","https://openalex.org/W3139299242","https://openalex.org/W3154612714","https://openalex.org/W3162724895","https://openalex.org/W3164608998","https://openalex.org/W3166434741","https://openalex.org/W3168195907","https://openalex.org/W3186883115","https://openalex.org/W3206383574","https://openalex.org/W3206744473","https://openalex.org/W3206959204","https://openalex.org/W3209198863","https://openalex.org/W3213536762","https://openalex.org/W4200380646","https://openalex.org/W4205909230","https://openalex.org/W4210851913","https://openalex.org/W4235508806","https://openalex.org/W4248947980","https://openalex.org/W4283272912","https://openalex.org/W4283688769","https://openalex.org/W4289783337","https://openalex.org/W4306173528","https://openalex.org/W4308436318","https://openalex.org/W4311751132","https://openalex.org/W4312186481","https://openalex.org/W4317499868","https://openalex.org/W4320914118","https://openalex.org/W4360868603","https://openalex.org/W4376121723","https://openalex.org/W6696826585"],"related_works":["https://openalex.org/W47352601","https://openalex.org/W2981957539","https://openalex.org/W4287378204","https://openalex.org/W2461489085","https://openalex.org/W4286950177","https://openalex.org/W4285337522","https://openalex.org/W3203498468","https://openalex.org/W2464866501","https://openalex.org/W2289852464","https://openalex.org/W2788261136"],"abstract_inverted_index":{"Harnessing":[0],"the":[1,31,34,58,63,73,130,139,198,226,240,266,273,281,285,291],"power":[2],"of":[3,12,65,151,182,203,205,248,265,276,284],"microbial":[4,38,66,155,304],"consortia":[5,39],"is":[6,27,117],"integral":[7],"to":[8,16,18,29,61,85,124,141,290],"a":[9,148,168,180,201,245],"diverse":[10],"range":[11],"sectors,":[13],"from":[14,68,159,211],"healthcare":[15],"biotechnology":[17],"environmental":[19],"remediation.":[20],"To":[21],"fully":[22],"realize":[23],"this":[24],"potential,":[25],"it":[26,116],"critical":[28],"understand":[30],"mechanisms":[32],"behind":[33],"interactions":[35],"that":[36,81,134],"structure":[37],"and":[40,46,112,127,187,222,236,243,251,287],"determine":[41],"their":[42,69,106,125,288],"functions.":[43],"Constraint-based":[44],"reconstruction":[45],"analysis":[47],"(COBRA)":[48],"approaches,":[49],"employing":[50],"genome-scale":[51],"metabolic":[52],"models":[53],"(GEMs),":[54],"have":[55,78,100],"emerged":[56],"as":[57,162],"state-of-the-art":[59],"tool":[60],"simulate":[62,86],"behavior":[64],"communities":[67,156,161],"constituent":[70],"genomes.":[71],"In":[72],"last":[74],"decade,":[75],"many":[76],"tools":[77,99,120,153,177,207,255,270],"been":[79,102],"developed":[80],"use":[82],"COBRA":[83],"approaches":[84,286],"multi-species":[87],"consortia,":[88],"under":[89],"either":[90],"steady-state,":[91],"dynamic,":[92],"or":[93],"spatiotemporally":[94],"varying":[95,262],"scenarios.":[96],"Yet,":[97],"these":[98,206],"not":[101],"systematically":[103],"evaluated":[104,174],"regarding":[105],"software":[107,192],"quality,":[108],"most":[109,131],"suitable":[110],"application,":[111],"predictive":[113],"power.":[114],"Hence,":[115],"uncertain":[118],"which":[119,172],"users":[121],"should":[122,136],"apply":[123],"system":[126],"what":[128],"are":[129],"urgent":[132],"directions":[133],"developers":[135],"take":[137],"in":[138,171,200,280],"future":[140,302],"improve":[142],"existing":[143],"capacities.":[144],"This":[145],"study":[146],"conducted":[147],"systematic":[149],"evaluation":[150],"COBRA-based":[152],"for":[154,191,225,239,254,300],"using":[157],"datasets":[158],"two-member":[160],"test":[163],"cases.":[164],"First,":[165],"we":[166,173,195,297],"performed":[167],"qualitative":[169],"assessment":[170],"24":[175],"published":[176],"based":[178],"on":[179],"list":[181],"FAIR":[183],"(Findability,":[184],"Accessibility,":[185],"Interoperability,":[186],"Reusability)":[188],"features":[189],"essential":[190],"quality.":[193],"Next,":[194],"quantitatively":[196],"tested":[197],"predictions":[199],"subset":[202],"14":[204],"against":[208],"experimental":[209],"data":[210],"three":[212],"different":[213,274],"case":[214],"studies:":[215],"a)":[216],"syngas":[217],"fermentation":[218,231],"by":[219],"C.":[220,223],"autoethanogenum":[221],"kluyveri":[224],"static":[227],"tools,":[228,242],"b)":[229],"glucose/xylose":[230],"with":[232],"engineered":[233],"E.":[234,249],"coli":[235,250],"S.":[237,252],"cerevisiae":[238],"dynamic":[241],"c)":[244],"Petri":[246],"dish":[247],"enterica":[253],"incorporating":[256],"spatiotemporal":[257],"variation.":[258],"Our":[259],"results":[260,292],"show":[261],"performance":[263],"levels":[264],"best":[267],"qualitatively":[268],"assessed":[269],"when":[271],"examining":[272],"categories":[275],"tools.":[277,306],"The":[278],"differences":[279],"mathematical":[282],"formulation":[283],"relation":[289],"were":[293],"also":[294],"discussed.":[295],"Ultimately,":[296],"provide":[298],"recommendations":[299],"refining":[301],"GEM":[303],"modeling":[305]},"counts_by_year":[{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":23},{"year":2023,"cited_by_count":3}],"updated_date":"2026-03-12T08:34:05.389933","created_date":"2025-10-10T00:00:00"}
