{"id":"https://openalex.org/W2889964088","doi":"https://doi.org/10.1093/bib/bby092","title":"Strategies for calibrating models of biology","display_name":"Strategies for calibrating models of biology","publication_year":2018,"publication_date":"2018-09-04","ids":{"openalex":"https://openalex.org/W2889964088","doi":"https://doi.org/10.1093/bib/bby092","mag":"2889964088","pmid":"https://pubmed.ncbi.nlm.nih.gov/30239570"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bby092","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bby092","pdf_url":null,"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":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071891762","display_name":"Mark Read","orcid":"https://orcid.org/0000-0002-1481-4780"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Mark N Read","raw_affiliation_strings":["University of Sydney, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Sydney, Australia","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024360871","display_name":"Kieran Alden","orcid":"https://orcid.org/0000-0003-4411-1776"},"institutions":[{"id":"https://openalex.org/I52099693","display_name":"University of York","ror":"https://ror.org/04m01e293","country_code":"GB","type":"education","lineage":["https://openalex.org/I52099693"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Kieran Alden","raw_affiliation_strings":["University of York, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of York, UK","institution_ids":["https://openalex.org/I52099693"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080582720","display_name":"Jon Timmis","orcid":"https://orcid.org/0000-0003-1055-0471"},"institutions":[{"id":"https://openalex.org/I52099693","display_name":"University of York","ror":"https://ror.org/04m01e293","country_code":"GB","type":"education","lineage":["https://openalex.org/I52099693"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jon Timmis","raw_affiliation_strings":["University of York, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of York, UK","institution_ids":["https://openalex.org/I52099693"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5105835589","display_name":"Paul S. Andrews","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Paul S Andrews","raw_affiliation_strings":["SimOmics Ltd, Suite 10 IT Centre, Innovation Way, York, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"SimOmics Ltd, Suite 10 IT Centre, Innovation Way, York, UK","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5071891762"],"corresponding_institution_ids":["https://openalex.org/I129604602"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.9063,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.73213706,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"21","issue":"1","first_page":"24","last_page":"35"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9973000288009644,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9955000281333923,"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/metric","display_name":"Metric (unit)","score":0.7415875792503357},{"id":"https://openalex.org/keywords/extrapolation","display_name":"Extrapolation","score":0.729802131652832},{"id":"https://openalex.org/keywords/calibration","display_name":"Calibration","score":0.7229586839675903},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6462341547012329},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.6239261627197266},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5759381055831909},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3742259442806244},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22264039516448975},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.18941548466682434},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09333449602127075}],"concepts":[{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.7415875792503357},{"id":"https://openalex.org/C132459708","wikidata":"https://www.wikidata.org/wiki/Q744069","display_name":"Extrapolation","level":2,"score":0.729802131652832},{"id":"https://openalex.org/C165838908","wikidata":"https://www.wikidata.org/wiki/Q736777","display_name":"Calibration","level":2,"score":0.7229586839675903},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6462341547012329},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6239261627197266},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5759381055831909},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3742259442806244},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22264039516448975},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.18941548466682434},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09333449602127075},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bby092","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bby092","pdf_url":null,"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:30239570","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30239570","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:eprints.whiterose.ac.uk:139634","is_oa":false,"landing_page_url":"https://orcid.org/0000-0003-1055-0471>","pdf_url":null,"source":{"id":"https://openalex.org/S4306400854","display_name":"White Rose Research Online (University of Leeds, The University of Sheffield, University of York)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2800616092","host_organization_name":"White Rose University Consortium","host_organization_lineage":["https://openalex.org/I2800616092"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:sure.sunderland.ac.uk:13936","is_oa":false,"landing_page_url":"http://sure.sunderland.ac.uk/view/creators/Read=3AMark=3A=3A.html>,","pdf_url":null,"source":{"id":"https://openalex.org/S4306402295","display_name":"Sunderland Repository (University of Sunderland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I5728261","host_organization_name":"University of Sunderland","host_organization_lineage":["https://openalex.org/I5728261"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320966","display_name":"University of Sydney","ror":"https://ror.org/0384j8v12"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":100,"referenced_works":["https://openalex.org/W9730082","https://openalex.org/W100464641","https://openalex.org/W969639195","https://openalex.org/W1516855283","https://openalex.org/W1535481092","https://openalex.org/W1577650155","https://openalex.org/W1585339076","https://openalex.org/W1752888260","https://openalex.org/W1768938576","https://openalex.org/W1885393191","https://openalex.org/W1894356981","https://openalex.org/W1909688331","https://openalex.org/W1921088252","https://openalex.org/W1956617022","https://openalex.org/W1965004987","https://openalex.org/W1965335252","https://openalex.org/W1965925125","https://openalex.org/W1967819170","https://openalex.org/W1970424517","https://openalex.org/W1971128281","https://openalex.org/W1973546808","https://openalex.org/W1977209720","https://openalex.org/W1979034309","https://openalex.org/W1983320831","https://openalex.org/W1993405608","https://openalex.org/W2000653200","https://openalex.org/W2002526701","https://openalex.org/W2005832207","https://openalex.org/W2008743602","https://openalex.org/W2009435671","https://openalex.org/W2011923356","https://openalex.org/W2021437384","https://openalex.org/W2022485595","https://openalex.org/W2034203593","https://openalex.org/W2034334510","https://openalex.org/W2035336687","https://openalex.org/W2038669746","https://openalex.org/W2040254201","https://openalex.org/W2043976521","https://openalex.org/W2044278781","https://openalex.org/W2045843506","https://openalex.org/W2047944059","https://openalex.org/W2048406724","https://openalex.org/W2055047552","https://openalex.org/W2071716711","https://openalex.org/W2073837702","https://openalex.org/W2075406130","https://openalex.org/W2090448257","https://openalex.org/W2092077482","https://openalex.org/W2099285880","https://openalex.org/W2104394228","https://openalex.org/W2104438296","https://openalex.org/W2120820364","https://openalex.org/W2126105956","https://openalex.org/W2126658193","https://openalex.org/W2128763542","https://openalex.org/W2132635773","https://openalex.org/W2136105491","https://openalex.org/W2146594373","https://openalex.org/W2152065574","https://openalex.org/W2152237445","https://openalex.org/W2152803686","https://openalex.org/W2162742070","https://openalex.org/W2165143211","https://openalex.org/W2167875025","https://openalex.org/W2212037558","https://openalex.org/W2230749025","https://openalex.org/W2297219066","https://openalex.org/W2338289743","https://openalex.org/W2338717024","https://openalex.org/W2346839593","https://openalex.org/W2394773481","https://openalex.org/W2417793772","https://openalex.org/W2421296032","https://openalex.org/W2506824871","https://openalex.org/W2507245649","https://openalex.org/W2508066343","https://openalex.org/W2513554053","https://openalex.org/W2520514472","https://openalex.org/W2594450422","https://openalex.org/W2605455618","https://openalex.org/W2767948091","https://openalex.org/W2768342046","https://openalex.org/W2779535723","https://openalex.org/W2790207806","https://openalex.org/W2801733428","https://openalex.org/W2802525560","https://openalex.org/W3020953368","https://openalex.org/W4205300089","https://openalex.org/W4211017114","https://openalex.org/W4230012481","https://openalex.org/W4230346472","https://openalex.org/W4234565636","https://openalex.org/W4243645092","https://openalex.org/W4251988601","https://openalex.org/W4285719527","https://openalex.org/W4388376074","https://openalex.org/W6660254288","https://openalex.org/W6698708696","https://openalex.org/W6833780757"],"related_works":["https://openalex.org/W1968270095","https://openalex.org/W4296478327","https://openalex.org/W1960072520","https://openalex.org/W2042397106","https://openalex.org/W4361730764","https://openalex.org/W1965029248","https://openalex.org/W2220129715","https://openalex.org/W2387596242","https://openalex.org/W2333625343","https://openalex.org/W2074627651"],"abstract_inverted_index":{"Computational":[0],"and":[1,25,33,61,83,141,194,211,229,282,287,306],"mathematical":[2],"modelling":[3,98,148],"has":[4],"become":[5],"a":[6,89,118,126,130,155,233,237,248,301],"valuable":[7],"tool":[8],"for":[9,170,188,254,271],"investigating":[10],"biological":[11,18,28,84,131,139,160,234],"systems.":[12],"Modelling":[13],"enables":[14],"prediction":[15],"of":[16,27,55,120,129,138,154,159,280,290,304],"how":[17,182,260,307],"components":[19],"interact":[20],"to":[21,31,92,97,105,122,199,217,226,244,299,308,312],"deliver":[22,314],"system-level":[23],"properties":[24,266],"extrapolation":[26],"system":[29],"performance":[30],"contexts":[32,54],"experimental":[34],"conditions":[35],"where":[36,173],"this":[37,296],"is":[38,95,100,208,242,298],"unknown.":[39],"A":[40,103],"model's":[41,127],"value":[42],"hinges":[43],"on":[44],"knowing":[45],"that":[46,80,111,231,262],"it":[47],"faithfully":[48],"represents":[49],"the":[50,53,147,152,200,212,218,278,288],"biology":[51],"under":[52],"use,":[56],"or":[57,162,240,317],"clearly":[58],"ascertaining":[59],"otherwise":[60],"thus":[62],"motivating":[63],"further":[64],"model":[65,77,82,156,174,213,235,256,291],"refinement.":[66],"These":[67],"qualities":[68],"are":[69,134,144,177],"evaluated":[70],"through":[71,88],"calibration,":[72,305],"typically":[73],"formulated":[74],"as":[75,86],"identifying":[76],"parameter":[78,175],"values":[79,176],"align":[81],"behaviours":[85,161],"measured":[87],"metric":[90,202],"applied":[91],"both.":[93],"Calibration":[94],"critical":[96],"but":[99],"often":[101],"underappreciated.":[102],"failure":[104],"appropriately":[106],"calibrate":[107],"risks":[108],"unrepresentative":[109],"models":[110,316],"generate":[112],"erroneous":[113],"insights.":[114],"Here,":[115],"we":[116,258,276],"review":[117],"suite":[119],"strategies":[121],"more":[123],"rigorously":[124],"challenge":[125],"representation":[128],"system.":[132],"All":[133],"motivated":[135],"by":[136],"features":[137],"systems,":[140,190],"illustrative":[142],"examples":[143],"drawn":[145],"from":[146],"literature.":[149],"We":[150,168,180,222],"examine":[151],"calibration":[153,171,207,219,286],"against":[157,236,247],"distributions":[158],"outcomes,":[163],"not":[164,268],"only":[165],"average":[166],"values.":[167],"argue":[169,230],"even":[172],"experimentally":[178],"ascertained.":[179],"explore":[181,259],"single":[183,238,249],"metrics":[184,261],"can":[185],"be":[186,269],"non-distinguishing":[187],"complex":[189],"with":[191],"multiple-component":[192],"dynamic":[193],"interaction":[195],"configurations":[196],"giving":[197],"rise":[198],"same":[201],"output.":[203],"Under":[204],"these":[205],"conditions,":[206],"insufficiently":[209],"constraining":[210],"non-identifiable:":[214],"multiple":[215],"solutions":[216],"problem":[220],"exist.":[221],"draw":[223],"an":[224],"analogy":[225],"curve":[227,245],"fitting":[228,246],"calibrating":[232],"experiment":[239],"context":[241],"akin":[243],"data":[250],"point.":[251],"Though":[252],"useful":[253],"communicating":[255],"results,":[257],"quantify":[263],"heavily":[264],"emergent":[265],"may":[267],"suitable":[270],"use":[272],"in":[273,285,295],"calibration.":[274],"Lastly,":[275],"consider":[277],"role":[279],"sensitivity":[281],"uncertainty":[283],"analysis":[284],"interpretation":[289],"results.":[292],"Our":[293],"goal":[294],"manuscript":[297],"encourage":[300],"deeper":[302],"consideration":[303],"increase":[309],"its":[310],"capacity":[311],"either":[313],"faithful":[315],"demonstrate":[318],"them":[319],"otherwise.":[320]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
