{"id":"https://openalex.org/W4210851913","doi":"https://doi.org/10.1093/bioinformatics/btac082","title":"Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities","display_name":"Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities","publication_year":2022,"publication_date":"2022-02-08","ids":{"openalex":"https://openalex.org/W4210851913","doi":"https://doi.org/10.1093/bioinformatics/btac082","pmid":"https://pubmed.ncbi.nlm.nih.gov/35157025"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac082","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac082","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/8/2367/43369971/btac082.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/38/8/2367/43369971/btac082.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074416067","display_name":"Almut Heinken","orcid":"https://orcid.org/0000-0001-6938-8072"},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Almut Heinken","raw_affiliation_strings":["Ryan Institute, National University of Galway , Galway, Ireland","School of Medicine, National University of Galway , Galway, Ireland"],"affiliations":[{"raw_affiliation_string":"Ryan Institute, National University of Galway , Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]},{"raw_affiliation_string":"School of Medicine, National University of Galway , Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074725115","display_name":"Ines Thiele","orcid":"https://orcid.org/0000-0002-8071-7110"},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]},{"id":"https://openalex.org/I27577105","display_name":"University College Cork","ror":"https://ror.org/03265fv13","country_code":"IE","type":"education","lineage":["https://openalex.org/I27577105"]},{"id":"https://openalex.org/I4210141138","display_name":"APC Microbiome Institute","ror":"https://ror.org/03f2ct267","country_code":"IE","type":"facility","lineage":["https://openalex.org/I4210141138"]}],"countries":["IE"],"is_corresponding":true,"raw_author_name":"Ines Thiele","raw_affiliation_strings":["APC Microbiome Ireland, University College Cork , Cork, Ireland","Division of Microbiology, National University of Galway , Galway, Ireland","Ryan Institute, National University of Galway , Galway, Ireland","School of Medicine, National University of Galway , Galway, Ireland"],"affiliations":[{"raw_affiliation_string":"APC Microbiome Ireland, University College Cork , Cork, Ireland","institution_ids":["https://openalex.org/I4210141138","https://openalex.org/I27577105"]},{"raw_affiliation_string":"Division of Microbiology, National University of Galway , Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]},{"raw_affiliation_string":"Ryan Institute, National University of Galway , Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]},{"raw_affiliation_string":"School of Medicine, National University of Galway , Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5074725115"],"corresponding_institution_ids":["https://openalex.org/I188760350","https://openalex.org/I27577105","https://openalex.org/I4210141138"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":4.4264,"has_fulltext":false,"cited_by_count":55,"citation_normalized_percentile":{"value":0.95838696,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"38","issue":"8","first_page":"2367","last_page":"2368"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9987999796867371,"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/T10066","display_name":"Gut microbiota and health","score":0.9987999796867371,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9728000164031982,"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/toolbox","display_name":"Toolbox","score":0.9218966960906982},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.8366492390632629},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.8357958197593689},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7893919944763184},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6100279092788696},{"id":"https://openalex.org/keywords/interrogation","display_name":"Interrogation","score":0.5413678884506226},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.5064867734909058},{"id":"https://openalex.org/keywords/constraint","display_name":"Constraint (computer-aided design)","score":0.4820000231266022},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.42062005400657654},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3567926287651062},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34737950563430786},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3338038921356201},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.21038299798965454},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.15306898951530457},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13317766785621643},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12538105249404907},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.0879773497581482},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08315214514732361}],"concepts":[{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.9218966960906982},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.8366492390632629},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.8357958197593689},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7893919944763184},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6100279092788696},{"id":"https://openalex.org/C2776240099","wikidata":"https://www.wikidata.org/wiki/Q327018","display_name":"Interrogation","level":2,"score":0.5413678884506226},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5064867734909058},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.4820000231266022},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.42062005400657654},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3567926287651062},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34737950563430786},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3338038921356201},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.21038299798965454},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.15306898951530457},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13317766785621643},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12538105249404907},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0879773497581482},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08315214514732361},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"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":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btac082","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac082","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/8/2367/43369971/btac082.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35157025","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35157025","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:null:10468/13175","is_oa":true,"landing_page_url":"http://hdl.handle.net/10468/13175","pdf_url":null,"source":{"id":"https://openalex.org/S4306401150","display_name":"Cork Open Research Archive (University College Cork, Ireland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210141138","host_organization_name":"APC Microbiome Institute","host_organization_lineage":["https://openalex.org/I4210141138"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Article (peer-reviewed)"},{"id":"pmh:oai:pubmedcentral.nih.gov:9004645","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9004645","pdf_url":null,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:www.lenus.ie:10147/643357","is_oa":false,"landing_page_url":"http://hdl.handle.net/10147/643357","pdf_url":null,"source":{"id":"https://openalex.org/S4306401756","display_name":"Lenus, The Irish Health Repository (Dr Steevens Hospital Library)","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":"England","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac082","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac082","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/8/2367/43369971/btac082.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1087416387","display_name":null,"funder_award_id":"1U19AG063744-01","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G3719789328","display_name":null,"funder_award_id":"1RF1AG058942-01","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"}],"funders":[{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4210851913.pdf","grobid_xml":"https://content.openalex.org/works/W4210851913.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W1978408474","https://openalex.org/W2559597060","https://openalex.org/W2762019694","https://openalex.org/W2951327715","https://openalex.org/W3029912146","https://openalex.org/W3100696020","https://openalex.org/W3164608998","https://openalex.org/W3164970195","https://openalex.org/W4256259619"],"related_works":["https://openalex.org/W2401316817","https://openalex.org/W1589588912","https://openalex.org/W2382804087","https://openalex.org/W2367830717","https://openalex.org/W2104637952","https://openalex.org/W2393800603","https://openalex.org/W2356812289","https://openalex.org/W2348542805","https://openalex.org/W2375055351","https://openalex.org/W2360050659"],"abstract_inverted_index":{"Microbiome":[0],"Modelling":[1],"Toolbox":[2,13],"and":[3],"tutorials":[4],"are":[5],"freely":[6],"available":[7],"as":[8],"part":[9],"of":[10],"the":[11],"COBRA":[12],"at":[14],"https://git.io/microbiomeModelingToolbox.":[15]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":15},{"year":2024,"cited_by_count":18},{"year":2023,"cited_by_count":14},{"year":2022,"cited_by_count":4}],"updated_date":"2026-04-15T08:11:43.952461","created_date":"2025-10-10T00:00:00"}
