{"id":"https://openalex.org/W2966282641","doi":"https://doi.org/10.1093/bioinformatics/btz598","title":"CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models","display_name":"CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models","publication_year":2019,"publication_date":"2019-07-25","ids":{"openalex":"https://openalex.org/W2966282641","doi":"https://doi.org/10.1093/bioinformatics/btz598","mag":"2966282641","pmid":"https://pubmed.ncbi.nlm.nih.gov/31359031"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz598","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz598","pdf_url":null,"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":null,"license_id":null,"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":"green","oa_url":"https://www.osti.gov/biblio/1563062","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008693461","display_name":"V\u00edtor Vieira","orcid":"https://orcid.org/0000-0001-9604-9586"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"V\u00edtor Vieira","raw_affiliation_strings":["Centre of Biological Engineering, University of Minho , Braga, Portugal"],"affiliations":[{"raw_affiliation_string":"Centre of Biological Engineering, University of Minho , Braga, Portugal","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040524717","display_name":"Miguel Rocha","orcid":"https://orcid.org/0000-0001-8439-8172"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Miguel Rocha","raw_affiliation_strings":["Centre of Biological Engineering, University of Minho , Braga, Portugal"],"affiliations":[{"raw_affiliation_string":"Centre of Biological Engineering, University of Minho , Braga, Portugal","institution_ids":["https://openalex.org/I99682543"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5008693461"],"corresponding_institution_ids":["https://openalex.org/I99682543"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6012,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.67164144,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"35","issue":"24","first_page":"5361","last_page":"5362"},"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":0.9952999949455261,"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/T11053","display_name":"Process Optimization and Integration","score":0.9851999878883362,"subfield":{"id":"https://openalex.org/subfields/2207","display_name":"Control and Systems 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":0.9184397459030151},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6813701391220093},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.6167877316474915},{"id":"https://openalex.org/keywords/constraint","display_name":"Constraint (computer-aided design)","score":0.4911184012889862},{"id":"https://openalex.org/keywords/pathway-analysis","display_name":"Pathway analysis","score":0.42960673570632935},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3680216670036316},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15966448187828064},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.15084776282310486},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13915157318115234},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.06881111860275269}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9184397459030151},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6813701391220093},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.6167877316474915},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.4911184012889862},{"id":"https://openalex.org/C2779230013","wikidata":"https://www.wikidata.org/wiki/Q25303877","display_name":"Pathway analysis","level":4,"score":0.42960673570632935},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3680216670036316},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15966448187828064},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.15084776282310486},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13915157318115234},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.06881111860275269},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":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":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","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":"D053858","descriptor_name":"Metabolic Networks and Pathways","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":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/btz598","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz598","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31359031","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31359031","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:osti.gov:1563062","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1563062","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:osti.gov:1582460","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1582460","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:repositorium.sdum.uminho.pt:1822/64166","is_oa":false,"landing_page_url":"http://hdl.handle.net/1822/64166","pdf_url":null,"source":{"id":"https://openalex.org/S4306400354","display_name":"Reposit\u00f3riUM (Universidade do Minho)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99682543","host_organization_name":"University of Minho","host_organization_lineage":["https://openalex.org/I99682543"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"journal article"},{"id":"pmh:oai:repositorium.uminho.pt:1822/64166","is_oa":false,"landing_page_url":"https://hdl.handle.net/1822/64166","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","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":null,"raw_type":"journal article"}],"best_oa_location":{"id":"pmh:oai:osti.gov:1563062","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1563062","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.8399999737739563}],"awards":[{"id":"https://openalex.org/G636768965","display_name":null,"funder_award_id":"UID/BIO/04469/2019","funder_id":"https://openalex.org/F4320337197","funder_display_name":"Nuclear Fuel Cycle and Supply Chain"},{"id":"https://openalex.org/G6922896651","display_name":null,"funder_award_id":"SFRH/BD/118657/2016","funder_id":"https://openalex.org/F4320337197","funder_display_name":"Nuclear Fuel Cycle and Supply Chain"},{"id":"https://openalex.org/G7452099291","display_name":null,"funder_award_id":"NORTE-01-0145-FEDER-000004","funder_id":"https://openalex.org/F4320337197","funder_display_name":"Nuclear Fuel Cycle and Supply Chain"}],"funders":[{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320337197","display_name":"Nuclear Fuel Cycle and Supply Chain","ror":"https://ror.org/05tj7dm33"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":8,"referenced_works":["https://openalex.org/W2011880165","https://openalex.org/W2046760236","https://openalex.org/W2048465561","https://openalex.org/W2094097101","https://openalex.org/W2098824895","https://openalex.org/W2127844534","https://openalex.org/W2144372567","https://openalex.org/W2561266760"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W4287027380","https://openalex.org/W1699080303","https://openalex.org/W2207495067","https://openalex.org/W1906486629","https://openalex.org/W2119683611","https://openalex.org/W2151866902","https://openalex.org/W2794999358"],"abstract_inverted_index":{"The":[0],"software":[1],"is":[2,25],"implemented":[3],"in":[4],"Python":[5],"3,":[6],"supported":[7,19],"on":[8],"most":[9],"operating":[10],"systems":[11],"and":[12],"requires":[13],"a":[14],"mixed-integer":[15],"linear":[16],"programming":[17],"optimizer":[18],"by":[20],"the":[21],"optlang":[22],"framework.":[23],"Source-code":[24],"available":[26],"at":[27],"https://github.com/BioSystemsUM/cobamp.":[28]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3}],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2025-10-10T00:00:00"}
