{"id":"https://openalex.org/W2285122494","doi":"https://doi.org/10.1093/bib/bbv096","title":"Computational resources and strategies to construct single-molecule metabolic models of microbial cells","display_name":"Computational resources and strategies to construct single-molecule metabolic models of microbial cells","publication_year":2015,"publication_date":"2015-10-28","ids":{"openalex":"https://openalex.org/W2285122494","doi":"https://doi.org/10.1093/bib/bbv096","mag":"2285122494","pmid":"https://pubmed.ncbi.nlm.nih.gov/26515531"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbv096","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv096","pdf_url":"https://academic.oup.com/bib/article-pdf/17/5/863/17486292/bbv096.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/17/5/863/17486292/bbv096.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055267949","display_name":"Denise Gameiro","orcid":null},"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"]},{"id":"https://openalex.org/I6289922","display_name":"Universidade de Vigo","ror":"https://ror.org/05rdf8595","country_code":"ES","type":"education","lineage":["https://openalex.org/I6289922"]}],"countries":["ES","PT"],"is_corresponding":true,"raw_author_name":"Denise Gameiro","raw_affiliation_strings":["Escuela Superior de Ingenier\u00b4\u0131a Informa\u00b4tica (ESEI), University of Vigo, Edificio Polite\u00b4cnico, Campus Universitario As Lagoas s/n 32004, Ourense, Spain; Centre of Biological Engineering (CEB),","University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal"],"affiliations":[{"raw_affiliation_string":"Escuela Superior de Ingenier\u00b4\u0131a Informa\u00b4tica (ESEI), University of Vigo, Edificio Polite\u00b4cnico, Campus Universitario As Lagoas s/n 32004, Ourense, Spain; Centre of Biological Engineering (CEB),","institution_ids":["https://openalex.org/I6289922"]},{"raw_affiliation_string":"University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067519995","display_name":"Mart\u00edn P\u00e9rez\u2010P\u00e9rez","orcid":"https://orcid.org/0000-0003-1349-6562"},"institutions":[{"id":"https://openalex.org/I6289922","display_name":"Universidade de Vigo","ror":"https://ror.org/05rdf8595","country_code":"ES","type":"education","lineage":["https://openalex.org/I6289922"]},{"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":["ES","PT"],"is_corresponding":false,"raw_author_name":"Mart\u00edn P\u00e9rez-P\u00e9rez","raw_affiliation_strings":["Escuela Superior de Ingenier\u00b4\u0131a Informa\u00b4tica (ESEI), University of Vigo, Edificio Polite\u00b4cnico, Campus Universitario As Lagoas s/n 32004, Ourense, Spain; Centre of Biological Engineering (CEB),","University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal"],"affiliations":[{"raw_affiliation_string":"Escuela Superior de Ingenier\u00b4\u0131a Informa\u00b4tica (ESEI), University of Vigo, Edificio Polite\u00b4cnico, Campus Universitario As Lagoas s/n 32004, Ourense, Spain; Centre of Biological Engineering (CEB),","institution_ids":["https://openalex.org/I6289922"]},{"raw_affiliation_string":"University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057813067","display_name":"Gael P\u00e9rez\u2010Rodr\u00edguez","orcid":"https://orcid.org/0000-0001-6740-3742"},"institutions":[{"id":"https://openalex.org/I6289922","display_name":"Universidade de Vigo","ror":"https://ror.org/05rdf8595","country_code":"ES","type":"education","lineage":["https://openalex.org/I6289922"]},{"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":["ES","PT"],"is_corresponding":false,"raw_author_name":"Gael P\u00e9rez-Rodr\u00edguez","raw_affiliation_strings":["Escuela Superior de Ingenier\u00b4\u0131a Informa\u00b4tica (ESEI), University of Vigo, Edificio Polite\u00b4cnico, Campus Universitario As Lagoas s/n 32004, Ourense, Spain; Centre of Biological Engineering (CEB),","University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal"],"affiliations":[{"raw_affiliation_string":"Escuela Superior de Ingenier\u00b4\u0131a Informa\u00b4tica (ESEI), University of Vigo, Edificio Polite\u00b4cnico, Campus Universitario As Lagoas s/n 32004, Ourense, Spain; Centre of Biological Engineering (CEB),","institution_ids":["https://openalex.org/I6289922"]},{"raw_affiliation_string":"University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052350894","display_name":"Gon\u00e7alo Monteiro","orcid":"https://orcid.org/0000-0003-4224-644X"},"institutions":[{"id":"https://openalex.org/I6289922","display_name":"Universidade de Vigo","ror":"https://ror.org/05rdf8595","country_code":"ES","type":"education","lineage":["https://openalex.org/I6289922"]},{"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":["ES","PT"],"is_corresponding":false,"raw_author_name":"Gon\u00e7alo Monteiro","raw_affiliation_strings":["Escuela Superior de Ingenier\u00b4\u0131a Informa\u00b4tica (ESEI), University of Vigo, Edificio Polite\u00b4cnico, Campus Universitario As Lagoas s/n 32004, Ourense, Spain; Centre of Biological Engineering (CEB),","University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal"],"affiliations":[{"raw_affiliation_string":"Escuela Superior de Ingenier\u00b4\u0131a Informa\u00b4tica (ESEI), University of Vigo, Edificio Polite\u00b4cnico, Campus Universitario As Lagoas s/n 32004, Ourense, Spain; Centre of Biological Engineering (CEB),","institution_ids":["https://openalex.org/I6289922"]},{"raw_affiliation_string":"University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035712663","display_name":"Nuno F. Azevedo","orcid":"https://orcid.org/0000-0001-5864-3250"},"institutions":[{"id":"https://openalex.org/I6289922","display_name":"Universidade de Vigo","ror":"https://ror.org/05rdf8595","country_code":"ES","type":"education","lineage":["https://openalex.org/I6289922"]},{"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":["ES","PT"],"is_corresponding":false,"raw_author_name":"Nuno F. Azevedo","raw_affiliation_strings":["Escuela Superior de Ingenier\u00b4\u0131a Informa\u00b4tica (ESEI), University of Vigo, Edificio Polite\u00b4cnico, Campus Universitario As Lagoas s/n 32004, Ourense, Spain; Centre of Biological Engineering (CEB),","University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal"],"affiliations":[{"raw_affiliation_string":"Escuela Superior de Ingenier\u00b4\u0131a Informa\u00b4tica (ESEI), University of Vigo, Edificio Polite\u00b4cnico, Campus Universitario As Lagoas s/n 32004, Ourense, Spain; Centre of Biological Engineering (CEB),","institution_ids":["https://openalex.org/I6289922"]},{"raw_affiliation_string":"University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033016354","display_name":"An\u00e1lia Louren\u00e7o","orcid":"https://orcid.org/0000-0001-8401-5362"},"institutions":[{"id":"https://openalex.org/I6289922","display_name":"Universidade de Vigo","ror":"https://ror.org/05rdf8595","country_code":"ES","type":"education","lineage":["https://openalex.org/I6289922"]},{"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":["ES","PT"],"is_corresponding":false,"raw_author_name":"An\u00e1lia Louren\u00e7o","raw_affiliation_strings":["Escuela Superior de Ingenier\u00b4\u0131a Informa\u00b4tica (ESEI), University of Vigo, Edificio Polite\u00b4cnico, Campus Universitario As Lagoas s/n 32004, Ourense, Spain; Centre of Biological Engineering (CEB),","University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal"],"affiliations":[{"raw_affiliation_string":"Escuela Superior de Ingenier\u00b4\u0131a Informa\u00b4tica (ESEI), University of Vigo, Edificio Polite\u00b4cnico, Campus Universitario As Lagoas s/n 32004, Ourense, Spain; Centre of Biological Engineering (CEB),","institution_ids":["https://openalex.org/I6289922"]},{"raw_affiliation_string":"University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal","institution_ids":["https://openalex.org/I99682543"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5055267949"],"corresponding_institution_ids":["https://openalex.org/I6289922","https://openalex.org/I99682543"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.6036,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.70200655,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"17","issue":"5","first_page":"863","last_page":"876"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994000196456909,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9994000196456909,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.995199978351593,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/biochemical-engineering","display_name":"Biochemical engineering","score":0.5849529504776001},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5229709148406982},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5178028345108032},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.49717047810554504},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.4830487370491028},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4623298645019531},{"id":"https://openalex.org/keywords/diffusion","display_name":"Diffusion","score":0.4554743766784668},{"id":"https://openalex.org/keywords/metabolic-pathway","display_name":"Metabolic pathway","score":0.43829232454299927},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4121336340904236},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3672230839729309},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.28847143054008484},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2782784402370453},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.21387335658073425},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.16103273630142212},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12999704480171204},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09507423639297485},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.08942079544067383}],"concepts":[{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.5849529504776001},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5229709148406982},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5178028345108032},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.49717047810554504},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.4830487370491028},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4623298645019531},{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.4554743766784668},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.43829232454299927},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4121336340904236},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3672230839729309},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.28847143054008484},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2782784402370453},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.21387335658073425},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.16103273630142212},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12999704480171204},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09507423639297485},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.08942079544067383},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","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":"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":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1093/bib/bbv096","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv096","pdf_url":"https://academic.oup.com/bib/article-pdf/17/5/863/17486292/bbv096.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26515531","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26515531","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:repositorio-aberto.up.pt:10216/105591","is_oa":true,"landing_page_url":"https://hdl.handle.net/10216/105591","pdf_url":"https://hdl.handle.net/10216/105591","source":{"id":"https://openalex.org/S4306401934","display_name":"Open Repository of the University of Porto (University of Porto)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I182534213","host_organization_name":"Universidade do Porto","host_organization_lineage":["https://openalex.org/I182534213"],"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:open-archive.highwire.org:bib:17/5/863","is_oa":false,"landing_page_url":"http://bib.oxfordjournals.org/cgi/content/short/17/5/863","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":"","raw_type":"TEXT"},{"id":"pmh:oai:repositorium.sdum.uminho.pt:1822/44665","is_oa":false,"landing_page_url":"http://hdl.handle.net/1822/44665","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":null},{"id":"pmh:oai:repositorium.uminho.pt:1822/44665","is_oa":false,"landing_page_url":"https://hdl.handle.net/1822/44665","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"},{"id":"pmh:oai:www.investigo.biblioteca.uvigo.es:11093/8300","is_oa":false,"landing_page_url":"http://hdl.handle.net/11093/8300","pdf_url":null,"source":{"id":"https://openalex.org/S4377196408","display_name":"Investigo Institutional repository of UVigo (Universidade de Vigo)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I6289922","host_organization_name":"Universidade de Vigo","host_organization_lineage":["https://openalex.org/I6289922"],"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":"article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbv096","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv096","pdf_url":"https://academic.oup.com/bib/article-pdf/17/5/863/17486292/bbv096.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2285122494.pdf","grobid_xml":"https://content.openalex.org/works/W2285122494.grobid-xml"},"referenced_works_count":89,"referenced_works":["https://openalex.org/W1504402896","https://openalex.org/W1565036272","https://openalex.org/W1581968111","https://openalex.org/W1586418342","https://openalex.org/W1873506857","https://openalex.org/W1918334909","https://openalex.org/W1965399445","https://openalex.org/W1965920457","https://openalex.org/W1966062610","https://openalex.org/W1969178306","https://openalex.org/W1972887106","https://openalex.org/W1975943954","https://openalex.org/W1976680692","https://openalex.org/W1976776824","https://openalex.org/W1984266961","https://openalex.org/W1986789040","https://openalex.org/W1996084127","https://openalex.org/W1996391065","https://openalex.org/W2003409413","https://openalex.org/W2004235182","https://openalex.org/W2006533898","https://openalex.org/W2015412290","https://openalex.org/W2018631534","https://openalex.org/W2022267063","https://openalex.org/W2024038403","https://openalex.org/W2028075953","https://openalex.org/W2028601571","https://openalex.org/W2030765885","https://openalex.org/W2031453406","https://openalex.org/W2032452417","https://openalex.org/W2034876354","https://openalex.org/W2035934220","https://openalex.org/W2036099201","https://openalex.org/W2036665047","https://openalex.org/W2040756306","https://openalex.org/W2041715593","https://openalex.org/W2041881366","https://openalex.org/W2050000908","https://openalex.org/W2052360207","https://openalex.org/W2054655080","https://openalex.org/W2055123264","https://openalex.org/W2059223531","https://openalex.org/W2064569009","https://openalex.org/W2065627978","https://openalex.org/W2068288772","https://openalex.org/W2076899675","https://openalex.org/W2077004593","https://openalex.org/W2077651691","https://openalex.org/W2089102241","https://openalex.org/W2090310656","https://openalex.org/W2092243213","https://openalex.org/W2096232803","https://openalex.org/W2096246094","https://openalex.org/W2101765772","https://openalex.org/W2103706175","https://openalex.org/W2103832753","https://openalex.org/W2105665788","https://openalex.org/W2108073693","https://openalex.org/W2114888488","https://openalex.org/W2116143213","https://openalex.org/W2127003259","https://openalex.org/W2127162389","https://openalex.org/W2128149907","https://openalex.org/W2131848047","https://openalex.org/W2135249385","https://openalex.org/W2136995378","https://openalex.org/W2140611297","https://openalex.org/W2149275261","https://openalex.org/W2151643303","https://openalex.org/W2152302868","https://openalex.org/W2152607628","https://openalex.org/W2153179692","https://openalex.org/W2158308821","https://openalex.org/W2160135160","https://openalex.org/W2162965868","https://openalex.org/W2163493106","https://openalex.org/W2169509065","https://openalex.org/W2169721219","https://openalex.org/W2170806980","https://openalex.org/W2171539493","https://openalex.org/W2180334400","https://openalex.org/W2228538196","https://openalex.org/W2285102836","https://openalex.org/W2739999456","https://openalex.org/W2785199982","https://openalex.org/W3124521395","https://openalex.org/W4239833133","https://openalex.org/W6646604252","https://openalex.org/W6683276083"],"related_works":["https://openalex.org/W2366107444","https://openalex.org/W4388145910","https://openalex.org/W1976205134","https://openalex.org/W2381570729","https://openalex.org/W4248336175","https://openalex.org/W3009369890","https://openalex.org/W2031260042","https://openalex.org/W2391445434","https://openalex.org/W207829213","https://openalex.org/W2315680351"],"abstract_inverted_index":{"Recent":[0],"computational":[1],"methodologies,":[2,30],"such":[3,29,173,197,209],"as":[4,45,107,174,198,210],"individual-based":[5],"modelling,":[6],"pave":[7],"the":[8,11,17,36,54,68,81,87,100,120,123,126,130,133,136,141,150,164,167,181,192],"way":[9],"to":[10,70,138,206],"search":[12],"for":[13,80,155],"explanatory":[14],"insight":[15],"into":[16],"collective":[18],"behaviour":[19],"of":[20,77,83,93,99,143,149,169,183],"molecules.":[21],"Many":[22],"reviews":[23],"offer":[24],"an":[25],"up-to-date":[26],"perspective":[27],"about":[28,35,115],"but":[31],"little":[32],"is":[33,67,97,204],"discussed":[34],"practical":[37],"information":[38,43,114,193],"requirements":[39],"involved.":[40],"The":[41,90],"biological":[42,171],"used":[44],"input":[46],"should":[47],"be":[48,139],"easily":[49],"and":[50,74,132,152,158,177,180,186,201,213],"routinely":[51],"determined":[52],"in":[53,61,104,163],"laboratory,":[55],"publicly":[56],"available":[57,78],"and,":[58],"preferably,":[59],"organized":[60],"programmatically":[62],"accessible":[63],"databases.":[64],"This":[65,110],"review":[66],"first":[69],"provide":[71],"a":[72],"systematic":[73],"comprehensive":[75],"overview":[76],"resources":[79],"modelling":[82],"metabolic":[84],"events":[85],"at":[86],"molecular":[88,175],"scale.":[89],"glycolysis":[91,127],"pathway":[92,128],"Escherichia":[94],"coli,":[95],"which":[96],"one":[98],"most":[101],"studied":[102],"pathways":[103],"Microbiology,":[105],"serves":[106],"case":[108],"study.":[109],"curation":[111],"addressed":[112],"structural":[113],"E.":[116],"coli":[117],"(i.e.":[118,135,146,160],"defining":[119],"simulation":[121,187,207],"environment),":[122],"reactions":[124],"forming":[125],"including":[129],"enzymes":[131,157],"metabolites":[134,159],"molecules":[137],"represented),":[140],"kinetics":[142],"each":[144],"reaction":[145],"behavioural":[147],"logic":[148],"molecules)":[151],"diffusion":[153,176,202],"parameters":[154],"all":[156],"molecule":[161],"movement":[162],"environment).":[165],"Furthermore,":[166],"interpretation":[168],"relevant":[170],"features,":[172],"enzyme":[178],"kinetics,":[179],"connection":[182],"experimental":[184],"determination":[185],"validation":[188],"are":[189],"detailed.":[190],"Notably,":[191],"from":[194],"classical":[195],"theories,":[196],"enzymatic":[199],"rates":[200],"coefficients,":[203],"translated":[205],"parameters,":[208],"collision":[211],"efficiency":[212],"particle":[214],"velocity.":[215]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
