{"id":"https://openalex.org/W2153251212","doi":"https://doi.org/10.1093/bioinformatics/btt018","title":"Improving the reuse of computational models through version control","display_name":"Improving the reuse of computational models through version control","publication_year":2013,"publication_date":"2013-01-18","ids":{"openalex":"https://openalex.org/W2153251212","doi":"https://doi.org/10.1093/bioinformatics/btt018","mag":"2153251212"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt018","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt018","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/6/742/48895502/bioinformatics_29_6_742.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/6/742/48895502/bioinformatics_29_6_742.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103188993","display_name":"Dagmar Waltemath","orcid":"https://orcid.org/0000-0002-5886-5563"},"institutions":[{"id":"https://openalex.org/I4210137766","display_name":"Institute for Advanced Study","ror":"https://ror.org/03xg85719","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210137766"]},{"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"]},{"id":"https://openalex.org/I26092322","display_name":"Stellenbosch University","ror":"https://ror.org/05bk57929","country_code":"ZA","type":"education","lineage":["https://openalex.org/I26092322"]}],"countries":["DE","ZA"],"is_corresponding":true,"raw_author_name":"Dagmar Waltemath","raw_affiliation_strings":["1 Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany, 2IT- and Media Center, University of Rostock, 18051 Rostock, Germany and 3Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa"],"affiliations":[{"raw_affiliation_string":"1 Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany, 2IT- and Media Center, University of Rostock, 18051 Rostock, Germany and 3Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa","institution_ids":["https://openalex.org/I26092322","https://openalex.org/I4210137766","https://openalex.org/I4665924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029731037","display_name":"Ron Henkel","orcid":"https://orcid.org/0000-0001-6211-2719"},"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"]},{"id":"https://openalex.org/I4210137766","display_name":"Institute for Advanced Study","ror":"https://ror.org/03xg85719","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210137766"]}],"countries":["DE","ZA"],"is_corresponding":false,"raw_author_name":"Ron Henkel","raw_affiliation_strings":["1 Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany, 2IT- and Media Center, University of Rostock, 18051 Rostock, Germany and 3Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa"],"affiliations":[{"raw_affiliation_string":"1 Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany, 2IT- and Media Center, University of Rostock, 18051 Rostock, Germany and 3Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa","institution_ids":["https://openalex.org/I26092322","https://openalex.org/I4210137766","https://openalex.org/I4665924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083573512","display_name":"Robert H\u00e4lke","orcid":null},"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"]},{"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/I4210137766","display_name":"Institute for Advanced Study","ror":"https://ror.org/03xg85719","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210137766"]}],"countries":["DE","ZA"],"is_corresponding":false,"raw_author_name":"Robert H\u00e4lke","raw_affiliation_strings":["1 Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany, 2IT- and Media Center, University of Rostock, 18051 Rostock, Germany and 3Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa"],"affiliations":[{"raw_affiliation_string":"1 Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany, 2IT- and Media Center, University of Rostock, 18051 Rostock, Germany and 3Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa","institution_ids":["https://openalex.org/I26092322","https://openalex.org/I4210137766","https://openalex.org/I4665924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046119695","display_name":"Martin Scharm","orcid":"https://orcid.org/0000-0003-4519-7030"},"institutions":[{"id":"https://openalex.org/I4210137766","display_name":"Institute for Advanced Study","ror":"https://ror.org/03xg85719","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210137766"]},{"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":"Martin Scharm","raw_affiliation_strings":["1 Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany, 2IT- and Media Center, University of Rostock, 18051 Rostock, Germany and 3Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa"],"affiliations":[{"raw_affiliation_string":"1 Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany, 2IT- and Media Center, University of Rostock, 18051 Rostock, Germany and 3Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa","institution_ids":["https://openalex.org/I26092322","https://openalex.org/I4210137766","https://openalex.org/I4665924"]}]},{"author_position":"last","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/I4210137766","display_name":"Institute for Advanced Study","ror":"https://ror.org/03xg85719","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210137766"]},{"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, 18051 Rostock, Germany, 2IT- and Media Center, University of Rostock, 18051 Rostock, Germany and 3Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa"],"affiliations":[{"raw_affiliation_string":"1 Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany, 2IT- and Media Center, University of Rostock, 18051 Rostock, Germany and 3Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa","institution_ids":["https://openalex.org/I26092322","https://openalex.org/I4210137766","https://openalex.org/I4665924"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5103188993"],"corresponding_institution_ids":["https://openalex.org/I26092322","https://openalex.org/I4210137766","https://openalex.org/I4665924"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.7781,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.909766,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"29","issue":"6","first_page":"742","last_page":"748"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9997000098228455,"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":0.9997000098228455,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9965999722480774,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9947999715805054,"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":0.8284637928009033},{"id":"https://openalex.org/keywords/reusability","display_name":"Reusability","score":0.7253437638282776},{"id":"https://openalex.org/keywords/reuse","display_name":"Reuse","score":0.6932637095451355},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.6250336170196533},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.5955876708030701},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5546980500221252},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.5415096879005432},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4898495376110077},{"id":"https://openalex.org/keywords/control","display_name":"Control (management)","score":0.45522603392601013},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.432670533657074},{"id":"https://openalex.org/keywords/conceptual-model","display_name":"Conceptual model","score":0.41725364327430725},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.329940527677536},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.2913883328437805},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23251602053642273},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.22396644949913025},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.156742125749588}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8284637928009033},{"id":"https://openalex.org/C137981799","wikidata":"https://www.wikidata.org/wiki/Q1369184","display_name":"Reusability","level":3,"score":0.7253437638282776},{"id":"https://openalex.org/C206588197","wikidata":"https://www.wikidata.org/wiki/Q846574","display_name":"Reuse","level":2,"score":0.6932637095451355},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.6250336170196533},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.5955876708030701},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5546980500221252},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.5415096879005432},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4898495376110077},{"id":"https://openalex.org/C2775924081","wikidata":"https://www.wikidata.org/wiki/Q55608371","display_name":"Control (management)","level":2,"score":0.45522603392601013},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.432670533657074},{"id":"https://openalex.org/C13606891","wikidata":"https://www.wikidata.org/wiki/Q2623243","display_name":"Conceptual model","level":2,"score":0.41725364327430725},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.329940527677536},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.2913883328437805},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23251602053642273},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.22396644949913025},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.156742125749588},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1093/bioinformatics/btt018","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt018","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/6/742/48895502/bioinformatics_29_6_742.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt018","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt018","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/6/742/48895502/bioinformatics_29_6_742.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"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/W2153251212.pdf","grobid_xml":"https://content.openalex.org/works/W2153251212.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W78068321","https://openalex.org/W1532171086","https://openalex.org/W1966722314","https://openalex.org/W1971060829","https://openalex.org/W1972793074","https://openalex.org/W1977796407","https://openalex.org/W1996195324","https://openalex.org/W1998125620","https://openalex.org/W2020561965","https://openalex.org/W2024797550","https://openalex.org/W2026692131","https://openalex.org/W2041956905","https://openalex.org/W2047632644","https://openalex.org/W2049998957","https://openalex.org/W2054902396","https://openalex.org/W2059715474","https://openalex.org/W2069157810","https://openalex.org/W2098769288","https://openalex.org/W2113218387","https://openalex.org/W2114124738","https://openalex.org/W2123783513","https://openalex.org/W2127950479","https://openalex.org/W2128763542","https://openalex.org/W2136317480","https://openalex.org/W2148329459","https://openalex.org/W2150908245","https://openalex.org/W2162744351","https://openalex.org/W2170122529","https://openalex.org/W2171926758","https://openalex.org/W2181917526","https://openalex.org/W2889443530","https://openalex.org/W2916475656","https://openalex.org/W3142746689","https://openalex.org/W4243013071","https://openalex.org/W6681837362","https://openalex.org/W6753879045","https://openalex.org/W6813711271"],"related_works":["https://openalex.org/W4385386698","https://openalex.org/W4235354490","https://openalex.org/W2381082207","https://openalex.org/W2025266532","https://openalex.org/W2136793911","https://openalex.org/W2143258726","https://openalex.org/W1971521465","https://openalex.org/W2377737135","https://openalex.org/W2100702185","https://openalex.org/W2355331657"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"Only":[2],"models":[3,14,38,120],"that":[4],"are":[5,31],"accessible":[6],"to":[7,33],"researchers":[8,89],"can":[9,90],"be":[10],"reused.":[11],"As":[12],"computational":[13],"evolve":[15],"over":[16],"time,":[17],"a":[18,26,133],"number":[19],"of":[20,25,76,82,104,109,118],"different":[21],"but":[22,39],"related":[23],"versions":[24],"model":[27,53,85,110],"exist.":[28],"Consequently,":[29],"tools":[30],"required":[32],"manage":[34],"not":[35],"only":[36],"well-curated":[37],"also":[40,154],"their":[41,123],"associated":[42],"versions.":[43,86],"Results:":[44],"In":[45,87],"this":[46,172],"work,":[47],"we":[48,68],"discuss":[49],"conceptual":[50],"requirements":[51],"for":[52,71,79,101,164],"version":[54,111,169],"control.":[55],"Focusing":[56],"on":[57,92],"XML":[58],"formats":[59],"such":[60],"as":[61],"Systems":[62],"Biology":[63],"Markup":[64],"Language":[65],"and":[66,74,78,121],"CellML,":[67],"present":[69],"methods":[70,131],"the":[72,80,102,116,129,157],"identification":[73],"explanation":[75],"differences":[77],"justification":[81],"changes":[83],"between":[84],"consequence,":[88],"reflect":[91],"these":[93],"changes,":[94],"which":[95,161],"in":[96,132,156,171],"turn":[97],"have":[98,127],"considerable":[99],"value":[100],"development":[103],"new":[105],"models.":[106],"The":[107],"implementation":[108],"control":[112],"will":[113],"therefore":[114],"foster":[115],"exploration":[117],"published":[119],"increase":[122],"reusability.":[124],"Availability:":[125],"We":[126],"implemented":[128],"proposed":[130],"software":[134],"library":[135],"called":[136],"Biochemical":[137,148],"Model":[138,149],"Version":[139,150],"Control":[140,151],"System.":[141],"It":[142],"is":[143,153,162,174],"freely":[144],"available":[145,163,175],"at":[146,166],"http://sems.uni-rostock.de/bives/.":[147],"System":[152],"integrated":[155],"online":[158],"application":[159],"BudHat,":[160],"testing":[165],"http://sems.uni-rostock.de/budhat/":[167],"(The":[168],"described":[170],"publication":[173],"from":[176],"http://budhat-demo.sems.uni-rostock.de/).":[177],"Contact:":[178],"dagmar.waltemath@uni-rostock.de":[179]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-06-24T00:00:00"}
