{"id":"https://openalex.org/W2949735890","doi":"https://doi.org/10.1093/bioinformatics/btz088","title":"Gsmodutils: a python based framework for test-driven genome scale metabolic model development","display_name":"Gsmodutils: a python based framework for test-driven genome scale metabolic model development","publication_year":2019,"publication_date":"2019-02-13","ids":{"openalex":"https://openalex.org/W2949735890","doi":"https://doi.org/10.1093/bioinformatics/btz088","mag":"2949735890","pmid":"https://pubmed.ncbi.nlm.nih.gov/30759197"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz088","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz088","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/18/3397/48975779/bioinformatics_35_18_3397.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/18/3397/48975779/bioinformatics_35_18_3397.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103028016","display_name":"James P. Gilbert","orcid":"https://orcid.org/0000-0003-2294-3459"},"institutions":[{"id":"https://openalex.org/I142263535","display_name":"University of Nottingham","ror":"https://ror.org/01ee9ar58","country_code":"GB","type":"education","lineage":["https://openalex.org/I142263535"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"James Gilbert","raw_affiliation_strings":["Synthetic Biology Research Centre, University of Nottingham , Nottingham, UK"],"raw_orcid":"https://orcid.org/0000-0003-2294-3459","affiliations":[{"raw_affiliation_string":"Synthetic Biology Research Centre, University of Nottingham , Nottingham, UK","institution_ids":["https://openalex.org/I142263535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029685571","display_name":"Nicole Pearcy","orcid":"https://orcid.org/0000-0001-8872-6436"},"institutions":[{"id":"https://openalex.org/I142263535","display_name":"University of Nottingham","ror":"https://ror.org/01ee9ar58","country_code":"GB","type":"education","lineage":["https://openalex.org/I142263535"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nicole Pearcy","raw_affiliation_strings":["Synthetic Biology Research Centre, University of Nottingham , Nottingham, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Synthetic Biology Research Centre, University of Nottingham , Nottingham, UK","institution_ids":["https://openalex.org/I142263535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056482122","display_name":"Rupert Norman","orcid":"https://orcid.org/0000-0003-4772-3698"},"institutions":[{"id":"https://openalex.org/I142263535","display_name":"University of Nottingham","ror":"https://ror.org/01ee9ar58","country_code":"GB","type":"education","lineage":["https://openalex.org/I142263535"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Rupert Norman","raw_affiliation_strings":["School of Biosciences, University of Nottingham, Sutton Bonington , Loughborough, UK","Synthetic Biology Research Centre, University of Nottingham , Nottingham, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biosciences, University of Nottingham, Sutton Bonington , Loughborough, UK","institution_ids":["https://openalex.org/I142263535"]},{"raw_affiliation_string":"Synthetic Biology Research Centre, University of Nottingham , Nottingham, UK","institution_ids":["https://openalex.org/I142263535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081500764","display_name":"Thomas Millat","orcid":"https://orcid.org/0000-0002-5023-4142"},"institutions":[{"id":"https://openalex.org/I142263535","display_name":"University of Nottingham","ror":"https://ror.org/01ee9ar58","country_code":"GB","type":"education","lineage":["https://openalex.org/I142263535"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Thomas Millat","raw_affiliation_strings":["Synthetic Biology Research Centre, University of Nottingham , Nottingham, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Synthetic Biology Research Centre, University of Nottingham , Nottingham, UK","institution_ids":["https://openalex.org/I142263535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032485641","display_name":"Klaus Winzer","orcid":"https://orcid.org/0000-0002-3956-8096"},"institutions":[{"id":"https://openalex.org/I142263535","display_name":"University of Nottingham","ror":"https://ror.org/01ee9ar58","country_code":"GB","type":"education","lineage":["https://openalex.org/I142263535"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Klaus Winzer","raw_affiliation_strings":["Synthetic Biology Research Centre, University of Nottingham , Nottingham, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Synthetic Biology Research Centre, University of Nottingham , Nottingham, UK","institution_ids":["https://openalex.org/I142263535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010038899","display_name":"John R. King","orcid":"https://orcid.org/0000-0002-6228-8375"},"institutions":[{"id":"https://openalex.org/I142263535","display_name":"University of Nottingham","ror":"https://ror.org/01ee9ar58","country_code":"GB","type":"education","lineage":["https://openalex.org/I142263535"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"John King","raw_affiliation_strings":["School of Mathematical Sciences, University of Nottingham , Nottingham, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematical Sciences, University of Nottingham , Nottingham, UK","institution_ids":["https://openalex.org/I142263535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051248114","display_name":"Charlie Hodgman","orcid":"https://orcid.org/0000-0001-5862-8296"},"institutions":[{"id":"https://openalex.org/I142263535","display_name":"University of Nottingham","ror":"https://ror.org/01ee9ar58","country_code":"GB","type":"education","lineage":["https://openalex.org/I142263535"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Charlie Hodgman","raw_affiliation_strings":["School of Biosciences, University of Nottingham, Sutton Bonington , Loughborough, UK","Synthetic Biology Research Centre, University of Nottingham , Nottingham, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biosciences, University of Nottingham, Sutton Bonington , Loughborough, UK","institution_ids":["https://openalex.org/I142263535"]},{"raw_affiliation_string":"Synthetic Biology Research Centre, University of Nottingham , Nottingham, UK","institution_ids":["https://openalex.org/I142263535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044949409","display_name":"Nigel P. Minton","orcid":"https://orcid.org/0000-0002-9277-1261"},"institutions":[{"id":"https://openalex.org/I142263535","display_name":"University of Nottingham","ror":"https://ror.org/01ee9ar58","country_code":"GB","type":"education","lineage":["https://openalex.org/I142263535"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nigel Minton","raw_affiliation_strings":["Synthetic Biology Research Centre, University of Nottingham , Nottingham, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Synthetic Biology Research Centre, University of Nottingham , Nottingham, UK","institution_ids":["https://openalex.org/I142263535"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003669992","display_name":"Jamie Twycross","orcid":"https://orcid.org/0000-0002-1684-0886"},"institutions":[{"id":"https://openalex.org/I142263535","display_name":"University of Nottingham","ror":"https://ror.org/01ee9ar58","country_code":"GB","type":"education","lineage":["https://openalex.org/I142263535"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Jamie Twycross","raw_affiliation_strings":["School of Computer Science, University of Nottingham , Nottingham, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, University of Nottingham , Nottingham, UK","institution_ids":["https://openalex.org/I142263535"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5003669992"],"corresponding_institution_ids":["https://openalex.org/I142263535"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":2658,"currency":"EUR","value_usd":2866},"fwci":0.2486,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.54660626,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"35","issue":"18","first_page":"3397","last_page":"3403"},"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/T11663","display_name":"Viral Infectious Diseases and Gene Expression in Insects","score":0.9972000122070312,"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":0.9968000054359436,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8219046592712402},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7267224788665771},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.540157675743103},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.4792444705963135},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4343162775039673},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.42528098821640015},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.4150146245956421},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3363233804702759},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.15837940573692322}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8219046592712402},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7267224788665771},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.540157675743103},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.4792444705963135},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4343162775039673},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.42528098821640015},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4150146245956421},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3363233804702759},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.15837940573692322},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems 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":false},{"descriptor_ui":"D060847","descriptor_name":"Metabolic Engineering","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":false},{"descriptor_ui":"D060847","descriptor_name":"Metabolic Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btz088","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz088","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/18/3397/48975779/bioinformatics_35_18_3397.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30759197","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30759197","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:6748746","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6748746","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:nottingham-repository.worktribe.com:1548123","is_oa":true,"landing_page_url":"https://nottingham-repository.worktribe.com/output/1548123","pdf_url":null,"source":{"id":"https://openalex.org/S4306402483","display_name":"Repository@Nottingham (University of Nottingham)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I142263535","host_organization_name":"University of Nottingham","host_organization_lineage":["https://openalex.org/I142263535"],"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":null,"raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz088","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz088","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/18/3397/48975779/bioinformatics_35_18_3397.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.6000000238418579,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G3559947993","display_name":null,"funder_award_id":"BB/L013940/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G3642178571","display_name":"SBRC NOTTINGHAM: Sustainable Routes to Platform Chemicals","funder_award_id":"BB/L013940/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G4575192214","display_name":null,"funder_award_id":"BB/K00283X/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G4949673100","display_name":"GASCHEM: Optimising industrial gas fermentation for commercial low-carbon fuel & chemical production through systems and synthetic biology approaches.","funder_award_id":"BB/L502030/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G5086451346","display_name":"GASCHEM: Optimising industrial gas fermentation for commercial low-carbon fuel & chemical production through systems and synthetic biology approaches","funder_award_id":"BB/K00283X/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G5621553766","display_name":null,"funder_award_id":"BB/L013940/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2949735890.pdf","grobid_xml":"https://content.openalex.org/works/W2949735890.grobid-xml"},"referenced_works_count":60,"referenced_works":["https://openalex.org/W174102300","https://openalex.org/W1507539036","https://openalex.org/W1534797499","https://openalex.org/W1952732684","https://openalex.org/W1965448844","https://openalex.org/W1975597731","https://openalex.org/W1976266924","https://openalex.org/W1977675219","https://openalex.org/W1996891655","https://openalex.org/W1997037290","https://openalex.org/W1999938932","https://openalex.org/W2008985174","https://openalex.org/W2009940763","https://openalex.org/W2026089579","https://openalex.org/W2036318837","https://openalex.org/W2048465561","https://openalex.org/W2051110041","https://openalex.org/W2059761552","https://openalex.org/W2067156145","https://openalex.org/W2072280409","https://openalex.org/W2078464013","https://openalex.org/W2082621456","https://openalex.org/W2085993965","https://openalex.org/W2089121522","https://openalex.org/W2096093282","https://openalex.org/W2100084634","https://openalex.org/W2108977450","https://openalex.org/W2112168274","https://openalex.org/W2131504364","https://openalex.org/W2133298156","https://openalex.org/W2143420371","https://openalex.org/W2143861551","https://openalex.org/W2147472054","https://openalex.org/W2148044817","https://openalex.org/W2150586932","https://openalex.org/W2150908245","https://openalex.org/W2156409537","https://openalex.org/W2160405086","https://openalex.org/W2167919951","https://openalex.org/W2169916860","https://openalex.org/W2179008870","https://openalex.org/W2179501783","https://openalex.org/W2202347610","https://openalex.org/W2202696179","https://openalex.org/W2267936092","https://openalex.org/W2272415328","https://openalex.org/W2296335794","https://openalex.org/W2403639486","https://openalex.org/W2419380513","https://openalex.org/W2592321159","https://openalex.org/W2623898396","https://openalex.org/W2625117623","https://openalex.org/W2802459091","https://openalex.org/W2949418748","https://openalex.org/W3047959390","https://openalex.org/W4211002602","https://openalex.org/W6632050423","https://openalex.org/W6693470995","https://openalex.org/W6697144307","https://openalex.org/W6782284924"],"related_works":["https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W4287027380","https://openalex.org/W1699080303","https://openalex.org/W4297799326","https://openalex.org/W4226323523","https://openalex.org/W2557718140","https://openalex.org/W67092138","https://openalex.org/W3201519406","https://openalex.org/W4225687299"],"abstract_inverted_index":{"MOTIVATION:":[0],"Genome":[1],"scale":[2,70,141],"metabolic":[3,13,142],"models":[4,27,94,121,184],"(GSMMs)":[5],"are":[6,18,85,192,237],"increasingly":[7],"important":[8],"for":[9,76,109,151],"systems":[10,111],"biology":[11],"and":[12,36,56,66,112,128,228],"engineering":[14],"research":[15],"as":[16],"they":[17],"capable":[19],"of":[20,28,34,59,68,134,155,183,207],"simulating":[21],"complex":[22],"steady-state":[23],"behaviour.":[24],"Constraints":[25],"based":[26,167],"this":[29,223],"form":[30],"can":[31],"include":[32],"thousands":[33],"reactions":[35],"metabolites,":[37],"with":[38,63],"many":[39],"crucial":[40],"pathways":[41],"that":[42],"only":[43],"become":[44],"activated":[45],"in":[46],"specific":[47],"simulation":[48],"settings.":[49],"However,":[50],"despite":[51],"their":[52,77],"widespread":[53],"use,":[54],"power":[55],"the":[57,64,124,152,163,173],"availability":[58],"tools":[60],"to":[61,97,100,123,138,162,196],"aid":[62],"construction":[65],"analysis":[67],"large":[69],"models,":[71],"little":[72],"methodology":[73,150],"is":[74,92,104,225],"suggested":[75],"continued":[78],"management.":[79],"For":[80],"example,":[81],"when":[82],"genome":[83,140],"annotations":[84],"updated":[86],"or":[87,201],"new":[88],"understanding":[89],"regarding":[90],"behaviour":[91],"discovered,":[93],"often":[95],"need":[96],"be":[98],"altered":[99],"reflect":[101],"this.":[102],"This":[103],"quickly":[105],"becoming":[106],"an":[107,135,178],"issue":[108],"industrial":[110],"synthetic":[113],"biotechnology":[114],"applications,":[115],"which":[116],"require":[117],"good":[118],"quality":[119],"reusable":[120],"integral":[122],"design,":[125],"build,":[126],"test":[127,187],"learn":[129],"cycle.":[130],"RESULTS:":[131],"As":[132],"part":[133],"ongoing":[136],"effort":[137],"improve":[139],"analysis,":[143],"we":[144,170],"have":[145,171],"developed":[146,172],"a":[147,204],"test-driven":[148,181],"development":[149],"continuous":[153],"integration":[154],"validation":[156],"data":[157,236],"from":[158,231],"different":[159,190,199],"sources.":[160],"Contributing":[161],"open":[164,226],"source":[165,227],"technology":[166],"around":[168],"COBRApy,":[169],"gsmodutils":[174],"modelling":[175],"framework":[176,220],"placing":[177],"emphasis":[179],"on":[180],"design":[182],"through":[185],"defined":[186],"cases.":[188],"Crucially,":[189],"conditions":[191],"configurable":[193],"allowing":[194],"users":[195],"examine":[197],"how":[198],"designs":[200],"curation":[202],"impact":[203],"wide":[205],"range":[206],"system":[208],"behaviours,":[209],"minimizing":[210],"error":[211],"between":[212],"model":[213],"versions.":[214],"AVAILABILITY":[215],"AND":[216],"IMPLEMENTATION:":[217],"The":[218],"software":[219],"described":[221],"within":[222],"paper":[224],"freely":[229],"available":[230,238],"http://github.com/SBRCNottingham/gsmodutils.":[232],"SUPPLEMENTARY":[233],"INFORMATION:":[234],"Supplementary":[235],"at":[239],"Bioinformatics":[240],"online.":[241]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2019-06-27T00:00:00"}