{"id":"https://openalex.org/W2179501783","doi":"https://doi.org/10.1093/bioinformatics/btv484","title":"An algorithm to detect and communicate the differences in computational models describing biological systems","display_name":"An algorithm to detect and communicate the differences in computational models describing biological systems","publication_year":2015,"publication_date":"2015-10-21","ids":{"openalex":"https://openalex.org/W2179501783","doi":"https://doi.org/10.1093/bioinformatics/btv484","mag":"2179501783","pmid":"https://pubmed.ncbi.nlm.nih.gov/26490504"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv484","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv484","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/4/563/49017437/bioinformatics_32_4_563.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/4/563/49017437/bioinformatics_32_4_563.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046119695","display_name":"Martin Scharm","orcid":"https://orcid.org/0000-0003-4519-7030"},"institutions":[{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Martin Scharm","raw_affiliation_strings":["1 Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany and","institution_ids":["https://openalex.org/I4665924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022724143","display_name":"Olaf Wolkenhauer","orcid":"https://orcid.org/0000-0001-6105-2937"},"institutions":[{"id":"https://openalex.org/I26092322","display_name":"Stellenbosch University","ror":"https://ror.org/05bk57929","country_code":"ZA","type":"education","lineage":["https://openalex.org/I26092322"]},{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE","ZA"],"is_corresponding":false,"raw_author_name":"Olaf Wolkenhauer","raw_affiliation_strings":["1 Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany and","2 Stellenbosch Institute for Advanced Study, Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany and","institution_ids":["https://openalex.org/I4665924"]},{"raw_affiliation_string":"2 Stellenbosch Institute for Advanced Study, Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa","institution_ids":["https://openalex.org/I26092322"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103188993","display_name":"Dagmar Waltemath","orcid":"https://orcid.org/0000-0002-5886-5563"},"institutions":[{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Dagmar Waltemath","raw_affiliation_strings":["1 Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany and","institution_ids":["https://openalex.org/I4665924"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5046119695"],"corresponding_institution_ids":["https://openalex.org/I4665924"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.6539,"has_fulltext":true,"cited_by_count":26,"citation_normalized_percentile":{"value":0.83868853,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"32","issue":"4","first_page":"563","last_page":"570"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.4885999858379364,"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":0.4885999858379364,"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/T13362","display_name":"Slime Mold and Myxomycetes Research","score":0.16349999606609344,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.07590000331401825,"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/computer-science","display_name":"Computer science","score":0.7008607983589172},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.49523845314979553},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3774716556072235},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3478989899158478}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7008607983589172},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.49523845314979553},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3774716556072235},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3478989899158478}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btv484","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv484","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/4/563/49017437/bioinformatics_32_4_563.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26490504","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26490504","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4743622","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4743622","pdf_url":null,"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/4/563","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/4/563","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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv484","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv484","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/4/563/49017437/bioinformatics_32_4_563.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1564535905","display_name":null,"funder_award_id":"FKZ 031","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G353144647","display_name":null,"funder_award_id":"031 6194","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G5739828583","display_name":null,"funder_award_id":"FKZ 0316194","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2179501783.pdf","grobid_xml":"https://content.openalex.org/works/W2179501783.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W174102300","https://openalex.org/W270576676","https://openalex.org/W1500560370","https://openalex.org/W1533573623","https://openalex.org/W1572313459","https://openalex.org/W1765549101","https://openalex.org/W1971060829","https://openalex.org/W1988545508","https://openalex.org/W2008985174","https://openalex.org/W2026692131","https://openalex.org/W2036318837","https://openalex.org/W2041956905","https://openalex.org/W2045808901","https://openalex.org/W2063463192","https://openalex.org/W2085851062","https://openalex.org/W2096435507","https://openalex.org/W2098769288","https://openalex.org/W2106352560","https://openalex.org/W2107249189","https://openalex.org/W2107572678","https://openalex.org/W2114124738","https://openalex.org/W2123783513","https://openalex.org/W2127950479","https://openalex.org/W2130200371","https://openalex.org/W2133938042","https://openalex.org/W2136043941","https://openalex.org/W2136393336","https://openalex.org/W2150908245","https://openalex.org/W2153100796","https://openalex.org/W2153251212","https://openalex.org/W2158378675","https://openalex.org/W2170122529","https://openalex.org/W2171926758","https://openalex.org/W2915063781","https://openalex.org/W4252803189","https://openalex.org/W6631796798","https://openalex.org/W6661641793","https://openalex.org/W6672085393","https://openalex.org/W6680206023"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829"],"abstract_inverted_index":{"MOTIVATION:":[0],"Repositories":[1],"support":[2],"the":[3,27,31,39,61,69,112,116,152,161,183,217],"reuse":[4,162],"of":[5,20,63,71,105,118,154,165,178,185,219],"models":[6,21,42,64,147,167],"and":[7,43,50,73,90,99,121,132,142,148,163,168,181,208],"ensure":[8],"transparency":[9],"about":[10],"results":[11,180],"in":[12,23,68,129,145,194,199],"publications":[13],"linked":[14],"to":[15,37,48,59,79,96,110,140,151,175,182],"those":[16],"models.":[17,52],"With":[18],"thousands":[19],"available":[22,204],"repositories,":[24],"such":[25],"as":[26,205],"BioModels":[28],"database":[29],"or":[30],"Physiome":[32],"Model":[33],"Repository,":[34],"a":[35,81,106,130,155],"framework":[36],"track":[38,80],"differences":[40,101],"between":[41,102],"their":[44],"versions":[45,104],"is":[46,127,197,202],"essential":[47],"compare":[49],"combine":[51],"Difference":[53],"detection":[54,70],"not":[55],"only":[56],"allows":[57],"users":[58],"study":[60],"history":[62],"but":[65],"also":[66],"helps":[67,139],"errors":[72],"inconsistencies.":[74],"Existing":[75],"repositories":[76],"lack":[77],"algorithms":[78],"model's":[82,156],"development":[83],"over":[84],"time.":[85],"RESULTS:":[86],"Focusing":[87],"on":[88],"SBML":[89],"CellML,":[91],"we":[92],"present":[93],"an":[94],"algorithm":[95,126],"accurately":[97],"detect":[98],"describe":[100],"coexisting":[103],"model":[107,186],"with":[108],"respect":[109],"(i)":[111],"models'":[113],"encoding,":[114],"(ii)":[115],"structure":[117],"biological":[119],"networks":[120],"(iii)":[122],"mathematical":[123],"expressions.":[124],"This":[125],"implemented":[128,198],"comprehensive":[131],"open":[133],"source":[134,206],"library":[135],"called":[136],"BiVeS.":[137,200],"BiVeS":[138,201,220],"identify":[141],"characterize":[143],"changes":[144],"computational":[146],"thereby":[149],"contributes":[150,174],"documentation":[153],"history.":[157],"Our":[158],"work":[159],"facilitates":[160],"extension":[164],"existing":[166],"supports":[169],"collaborative":[170],"modelling.":[171],"Finally,":[172],"it":[173],"better":[176],"reproducibility":[177],"modelling":[179],"challenge":[184],"provenance.":[187],"AVAILABILITY":[188],"AND":[189],"IMPLEMENTATION:":[190],"The":[191,212],"workflow":[192],"described":[193],"this":[195],"article":[196],"freely":[203],"code":[207],"binary":[209],"from":[210],"sems.uni-rostock.de.":[211],"web":[213],"interface":[214],"BudHat":[215],"demonstrates":[216],"capabilities":[218],"at":[221],"budhat.sems.uni-rostock.de.":[222]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2016,"cited_by_count":8}],"updated_date":"2026-08-09T07:27:16.801131","created_date":"2025-10-10T00:00:00"}
