{"id":"https://openalex.org/W4393279188","doi":"https://doi.org/10.1093/bioinformatics/btae153","title":"PyCoMo: a python package for community metabolic model creation and analysis","display_name":"PyCoMo: a python package for community metabolic model creation and analysis","publication_year":2024,"publication_date":"2024-03-25","ids":{"openalex":"https://openalex.org/W4393279188","doi":"https://doi.org/10.1093/bioinformatics/btae153","pmid":"https://pubmed.ncbi.nlm.nih.gov/38532295"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae153","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae153","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae153/57097749/btae153.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae153/57097749/btae153.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013941557","display_name":"Michael Predl","orcid":"https://orcid.org/0000-0002-3556-4661"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Michael Predl","raw_affiliation_strings":["Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna , 1030 Vienna, Austria","Doctoral School in Microbiology and Environmental Science, University of Vienna , 1030 Vienna, Austria","University of Vienna Doctoral School in Microbiology and Environmental Science, , Vienna, Austria","University of Vienna Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, , Vienna, Austria"],"raw_orcid":"https://orcid.org/0000-0002-3556-4661","affiliations":[{"raw_affiliation_string":"Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna , 1030 Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]},{"raw_affiliation_string":"Doctoral School in Microbiology and Environmental Science, University of Vienna , 1030 Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]},{"raw_affiliation_string":"University of Vienna Doctoral School in Microbiology and Environmental Science, , Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]},{"raw_affiliation_string":"University of Vienna Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, , Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081981197","display_name":"Marianne Mie\u00dfkes","orcid":"https://orcid.org/0009-0000-4305-5392"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]},{"id":"https://openalex.org/I4210138243","display_name":"Austrian Centre of Industrial Biotechnology (Austria)","ror":"https://ror.org/03dm7dd93","country_code":"AT","type":"company","lineage":["https://openalex.org/I4210138243"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Marianne Mie\u00dfkes","raw_affiliation_strings":["Austrian Centre of Industrial Biotechnology , 1190 Vienna, Austria","Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna , 1090 Vienna, Austria","Austrian Centre of Industrial Biotechnology , Vienna, Austria","University of Vienna Department of Analytical Chemistry, Faculty of Chemistry, , Vienna, Austria"],"raw_orcid":"https://orcid.org/0009-0000-4305-5392","affiliations":[{"raw_affiliation_string":"Austrian Centre of Industrial Biotechnology , 1190 Vienna, Austria","institution_ids":["https://openalex.org/I4210138243"]},{"raw_affiliation_string":"Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna , 1090 Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]},{"raw_affiliation_string":"Austrian Centre of Industrial Biotechnology , Vienna, Austria","institution_ids":["https://openalex.org/I4210138243"]},{"raw_affiliation_string":"University of Vienna Department of Analytical Chemistry, Faculty of Chemistry, , Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051653794","display_name":"Thomas Rattei","orcid":"https://orcid.org/0000-0002-0592-7791"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Thomas Rattei","raw_affiliation_strings":["Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna , 1030 Vienna, Austria","Doctoral School in Microbiology and Environmental Science, University of Vienna , 1030 Vienna, Austria","University of Vienna Doctoral School in Microbiology and Environmental Science, , Vienna, Austria","University of Vienna Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, , Vienna, Austria"],"raw_orcid":"https://orcid.org/0000-0002-0592-7791","affiliations":[{"raw_affiliation_string":"Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna , 1030 Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]},{"raw_affiliation_string":"Doctoral School in Microbiology and Environmental Science, University of Vienna , 1030 Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]},{"raw_affiliation_string":"University of Vienna Doctoral School in Microbiology and Environmental Science, , Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]},{"raw_affiliation_string":"University of Vienna Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, , Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053663717","display_name":"J\u00fcrgen Zanghellini","orcid":"https://orcid.org/0000-0002-1964-2455"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]},{"id":"https://openalex.org/I4210138243","display_name":"Austrian Centre of Industrial Biotechnology (Austria)","ror":"https://ror.org/03dm7dd93","country_code":"AT","type":"company","lineage":["https://openalex.org/I4210138243"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"J\u00fcrgen Zanghellini","raw_affiliation_strings":["Austrian Centre of Industrial Biotechnology , 1190 Vienna, Austria","Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna , 1090 Vienna, Austria","Austrian Centre of Industrial Biotechnology , Vienna, Austria","University of Vienna Department of Analytical Chemistry, Faculty of Chemistry, , Vienna, Austria"],"raw_orcid":"https://orcid.org/0000-0002-1964-2455","affiliations":[{"raw_affiliation_string":"Austrian Centre of Industrial Biotechnology , 1190 Vienna, Austria","institution_ids":["https://openalex.org/I4210138243"]},{"raw_affiliation_string":"Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna , 1090 Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]},{"raw_affiliation_string":"Austrian Centre of Industrial Biotechnology , Vienna, Austria","institution_ids":["https://openalex.org/I4210138243"]},{"raw_affiliation_string":"University of Vienna Department of Analytical Chemistry, Faculty of Chemistry, , Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5051653794","https://openalex.org/A5053663717"],"corresponding_institution_ids":["https://openalex.org/I129774422","https://openalex.org/I4210138243"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.1759,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.9231673,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"40","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.8568999767303467,"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":0.8568999767303467,"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/T10284","display_name":"Anaerobic Digestion and Biogas Production","score":0.03660000115633011,"subfield":{"id":"https://openalex.org/subfields/2215","display_name":"Building and Construction"},"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/T12688","display_name":"Microbial metabolism and enzyme function","score":0.03550000116229057,"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/python","display_name":"Python (programming language)","score":0.9439254999160767},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7001104950904846},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.6953612565994263},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.5925832390785217},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4114443063735962},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3463016152381897},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34127819538116455}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9439254999160767},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7001104950904846},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.6953612565994263},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.5925832390785217},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4114443063735962},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3463016152381897},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34127819538116455}],"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":"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":"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae153","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae153","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae153/57097749/btae153.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:38532295","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38532295","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:10990682","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10990682","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10990682/pdf/btae153.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae153","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae153","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae153/57097749/btae153.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":[],"awards":[{"id":"https://openalex.org/G1493680203","display_name":"Microbial symbioses in dynamic environments: Metabolic interplay and novel interactions (MAINTAIN)","funder_award_id":"DOC 69","funder_id":"https://openalex.org/F4320321181","funder_display_name":"Austrian Science Fund"}],"funders":[{"id":"https://openalex.org/F4320310617","display_name":"Klima- und Energiefonds","ror":"https://ror.org/044ym4p17"},{"id":"https://openalex.org/F4320321181","display_name":"Austrian Science Fund","ror":"https://ror.org/013tf3c58"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4393279188.pdf"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W2048465561","https://openalex.org/W2168465568","https://openalex.org/W2202347610","https://openalex.org/W2273147197","https://openalex.org/W2397950241","https://openalex.org/W2791048175","https://openalex.org/W2914170023","https://openalex.org/W2949418748","https://openalex.org/W3002175424","https://openalex.org/W3080133182","https://openalex.org/W3134142139","https://openalex.org/W3164608998","https://openalex.org/W3166434741","https://openalex.org/W3181417587","https://openalex.org/W4200555280","https://openalex.org/W4241630616","https://openalex.org/W4317499868"],"related_works":["https://openalex.org/W2207495067","https://openalex.org/W1906486629","https://openalex.org/W4389426664","https://openalex.org/W3000262071","https://openalex.org/W4380871953","https://openalex.org/W2763172433","https://openalex.org/W2566205467","https://openalex.org/W3012616639","https://openalex.org/W3126000805","https://openalex.org/W3198565742"],"abstract_inverted_index":{"SUMMARY:":[0],"PyCoMo":[1,91],"is":[2,92],"a":[3,39,49,62,80],"python":[4],"package":[5],"for":[6],"quick":[7],"and":[8,53,58,105],"easy":[9],"generation":[10],"of":[11,67],"genome-scale":[12],"compartmentalized":[13],"community":[14,46,63,85],"metabolic":[15,64,86],"models":[16,27],"that":[17],"are":[18],"compliant":[19],"with":[20],"current":[21],"openCOBRA":[22],"file":[23],"formats.":[24],"The":[25],"resulting":[26],"can":[28],"be":[29],"used":[30],"to":[31],"predict":[32],"(i)":[33],"the":[34,44,68,101],"maximum":[35],"growth":[36,51],"rate":[37],"at":[38,48,99],"given":[40,50],"abundance":[41,69],"profile,":[42],"(ii)":[43],"feasible":[45],"compositions":[47],"rate,":[52],"(iii)":[54],"all":[55],"exchange":[56],"metabolites":[57],"cross-feeding":[59],"interactions":[60],"in":[61,79],"model":[65],"independent":[66],"profile;":[70],"we":[71],"demonstrate":[72],"PyCoMo's":[73],"capability":[74],"by":[75],"analysing":[76],"methane":[77],"production":[78],"previously":[81],"published":[82],"simplified":[83],"biogas":[84],"model.":[87],"AVAILABILITY":[88],"AND":[89],"IMPLEMENTATION:":[90],"freely":[93],"available":[94],"under":[95],"an":[96],"MIT":[97],"licence":[98],"http://github.com/univieCUBE/PyCoMo,":[100],"Python":[102],"Package":[103],"Index,":[104],"Zenodo.":[106]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":6}],"updated_date":"2026-07-11T18:08:03.149640","created_date":"2025-10-10T00:00:00"}
