{"id":"https://openalex.org/W4391540638","doi":"https://doi.org/10.1515/jib-2023-0048","title":"MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps","display_name":"MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps","publication_year":2024,"publication_date":"2024-02-05","ids":{"openalex":"https://openalex.org/W4391540638","doi":"https://doi.org/10.1515/jib-2023-0048","pmid":"https://pubmed.ncbi.nlm.nih.gov/38314776"},"language":"en","primary_location":{"id":"doi:10.1515/jib-2023-0048","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2023-0048","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2023-0048/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.degruyter.com/document/doi/10.1515/jib-2023-0048/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090135477","display_name":"Sahar Aghakhani","orcid":"https://orcid.org/0000-0002-6392-4687"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210126360","display_name":"Centre Inria de Saclay","ror":"https://ror.org/0315e5x55","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210126360"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Sahar Aghakhani","raw_affiliation_strings":["GenHotel \u2013 European Research Laboratory for Rheumatoid Arthritis , Univ. Evry, Univ. Paris-Saclay , Evry , France","Lifeware Group , Inria Saclay , Palaiseau , France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GenHotel \u2013 European Research Laboratory for Rheumatoid Arthritis , Univ. Evry, Univ. Paris-Saclay , Evry , France","institution_ids":["https://openalex.org/I277688954"]},{"raw_affiliation_string":"Lifeware Group , Inria Saclay , Palaiseau , France","institution_ids":["https://openalex.org/I4210126360"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050740875","display_name":"Anna Niarakis","orcid":"https://orcid.org/0000-0002-9687-7426"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210126360","display_name":"Centre Inria de Saclay","ror":"https://ror.org/0315e5x55","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210126360"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Anna Niarakis","raw_affiliation_strings":["GenHotel \u2013 European Research Laboratory for Rheumatoid Arthritis , Univ. Evry, Univ. Paris-Saclay , Evry , France","Lifeware Group , Inria Saclay , Palaiseau , France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GenHotel \u2013 European Research Laboratory for Rheumatoid Arthritis , Univ. Evry, Univ. Paris-Saclay , Evry , France","institution_ids":["https://openalex.org/I277688954"]},{"raw_affiliation_string":"Lifeware Group , Inria Saclay , Palaiseau , France","institution_ids":["https://openalex.org/I4210126360"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003525513","display_name":"Sylvain Soliman","orcid":"https://orcid.org/0000-0001-5525-7418"},"institutions":[{"id":"https://openalex.org/I4210126360","display_name":"Centre Inria de Saclay","ror":"https://ror.org/0315e5x55","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210126360"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Sylvain Soliman","raw_affiliation_strings":["Lifeware Group , Inria Saclay , Palaiseau , France","Lifeware - Computational systems biology and optimization (France)"],"raw_orcid":"https://orcid.org/0000-0001-5525-7418","affiliations":[{"raw_affiliation_string":"Lifeware Group , Inria Saclay , Palaiseau , France","institution_ids":["https://openalex.org/I4210126360"]},{"raw_affiliation_string":"Lifeware - Computational systems biology and optimization (France)","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5003525513"],"corresponding_institution_ids":["https://openalex.org/I4210126360"],"apc_list":{"value":1000,"currency":"EUR","value_usd":1082},"apc_paid":{"value":1000,"currency":"EUR","value_usd":1082},"fwci":0.4665,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.58399905,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":96},"biblio":{"volume":"21","issue":"1","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":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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9987000226974487,"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":0.9943000078201294,"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/computer-science","display_name":"Computer science","score":0.7252905964851379},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.651414155960083},{"id":"https://openalex.org/keywords/notation","display_name":"Notation","score":0.6021723747253418},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5842510461807251},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.574799656867981},{"id":"https://openalex.org/keywords/asynchronous-communication","display_name":"Asynchronous communication","score":0.5690567493438721},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5438388586044312},{"id":"https://openalex.org/keywords/flux-balance-analysis","display_name":"Flux balance analysis","score":0.5426149964332581},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.526715099811554},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.48957332968711853},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40199682116508484},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.220225989818573},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17885810136795044},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09657120704650879}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7252905964851379},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.651414155960083},{"id":"https://openalex.org/C45357846","wikidata":"https://www.wikidata.org/wiki/Q2001982","display_name":"Notation","level":2,"score":0.6021723747253418},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5842510461807251},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.574799656867981},{"id":"https://openalex.org/C151319957","wikidata":"https://www.wikidata.org/wiki/Q752739","display_name":"Asynchronous communication","level":2,"score":0.5690567493438721},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5438388586044312},{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.5426149964332581},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.526715099811554},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.48957332968711853},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40199682116508484},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.220225989818573},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17885810136795044},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09657120704650879},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C94375191","wikidata":"https://www.wikidata.org/wiki/Q11205","display_name":"Arithmetic","level":1,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.0},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"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":"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":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":"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":"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":"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},{"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},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1515/jib-2023-0048","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2023-0048","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2023-0048/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38314776","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38314776","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":"Journal of integrative bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:HAL:hal-04439008v1","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-04439008","pdf_url":"https://inria.hal.science/hal-04439008v1/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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":"Journal of Integrative Bioinformatics, 2024, 21 (1), pp.20230048. &#x27E8;10.1515/jib-2023-0048&#x27E9;","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11293895","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11293895","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11293895/pdf/jib-21-1-jib-2023-0048.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":"J Integr Bioinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:205e0bb2232b4955ab2d07cad6f0a773","is_oa":true,"landing_page_url":"https://doaj.org/article/205e0bb2232b4955ab2d07cad6f0a773","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Integrative Bioinformatics, Vol 21, Iss 1, Pp 1-13 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1515/jib-2023-0048","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2023-0048","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2023-0048/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.8199999928474426}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4391540638.pdf","grobid_xml":"https://content.openalex.org/works/W4391540638.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1969547738","https://openalex.org/W1998633945","https://openalex.org/W2048465561","https://openalex.org/W2078355959","https://openalex.org/W2117364474","https://openalex.org/W2149991291","https://openalex.org/W2150908245","https://openalex.org/W2202347610","https://openalex.org/W2216418212","https://openalex.org/W2796191283","https://openalex.org/W2949726389","https://openalex.org/W2950329335","https://openalex.org/W2950427358","https://openalex.org/W2977870980","https://openalex.org/W3025361835","https://openalex.org/W3080133182","https://openalex.org/W3090947236","https://openalex.org/W3201713003","https://openalex.org/W4206447491","https://openalex.org/W4283078612","https://openalex.org/W4285013431","https://openalex.org/W4312190224","https://openalex.org/W4384564578","https://openalex.org/W4386013523"],"related_works":["https://openalex.org/W4241916770","https://openalex.org/W2374260038","https://openalex.org/W1971436540","https://openalex.org/W2020641517","https://openalex.org/W2216418212","https://openalex.org/W3033588432","https://openalex.org/W2075919068","https://openalex.org/W2540651481","https://openalex.org/W2047632644","https://openalex.org/W2157084984"],"abstract_inverted_index":{"Molecular":[0],"interaction":[1],"maps":[2],"(MIMs)":[3],"are":[4,35],"static":[5],"graphical":[6],"representations":[7],"depicting":[8],"complex":[9],"biochemical":[10],"networks":[11,172],"that":[12,60],"can":[13,44],"be":[14],"formalized":[15],"using":[16],"one":[17],"of":[18,26,30,39,64,85,95,111,150,160,178,192],"the":[19,62,83,102,109,119,151,190,193],"Systems":[20],"Biology":[21],"Graphical":[22],"Notation":[23],"languages.":[24],"Regardless":[25],"their":[27],"extensive":[28],"coverage":[29],"various":[31],"biological":[32,166],"processes,":[33,90],"they":[34],"limited":[36],"in":[37,147,163],"terms":[38,191],"dynamic":[40,50],"insights.":[41],"However,":[42],"MIMs":[43,71],"serve":[45],"as":[46],"templates":[47],"for":[48],"developing":[49],"computational":[51],"models.":[52],"We":[53],"present":[54],"MetaLo,":[55],"an":[56],"open-source":[57],"Python":[58],"package":[59],"enables":[61,146],"coupling":[63],"Boolean":[65,103,129],"models":[66,130,134],"inferred":[67],"from":[68],"process":[69],"description":[70],"with":[72,174],"generic":[73,120,170],"core":[74],"metabolic":[75,92,115,121,133,171,182],"networks.":[76,183],"MetaLo":[77,100,123,145,184],"provides":[78],"a":[79,158],"framework":[80,143],"to":[81,117,126,168],"study":[82],"impact":[84],"signaling":[86],"cascades,":[87],"gene":[88],"regulation":[89],"and":[91,113,131,154],"flux":[93],"distribution":[94],"central":[96],"energy":[97],"production":[98],"pathways.":[99],"computes":[101],"model's":[104],"asynchronous":[105],"asymptotic":[106],"behavior,":[107],"through":[108],"identification":[110],"trap-spaces,":[112],"extracts":[114],"constraints":[116],"contextualize":[118,169],"network.":[122],"is":[124,185],"able":[125],"handle":[127],"large-scale":[128],"genome-scale":[132],"without":[135],"requiring":[136],"kinetic":[137],"information":[138],"or":[139],"manual":[140],"tuning.":[141],"The":[142],"behind":[144],"depth":[148],"analysis":[149],"regulatory":[152],"model,":[153],"may":[155],"allow":[156],"tackling":[157],"lack":[159],"omics":[161],"data":[162],"poorly":[164],"addressed":[165],"fields":[167],"along":[173],"improper":[175],"automatic":[176],"reconstructions":[177],"cell-":[179],"and/or":[180],"disease-specific":[181],"available":[186],"at":[187],"https://pypi.org/project/metalo/":[188],"under":[189],"GNU":[194],"General":[195],"Public":[196],"License":[197],"v3.":[198]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2025-10-10T00:00:00"}
