{"id":"https://openalex.org/W3206315495","doi":"https://doi.org/10.1515/hsz-2021-0393","title":"On the reproducibility of enzyme reactions and kinetic modelling","display_name":"On the reproducibility of enzyme reactions and kinetic modelling","publication_year":2022,"publication_date":"2022-03-31","ids":{"openalex":"https://openalex.org/W3206315495","doi":"https://doi.org/10.1515/hsz-2021-0393","mag":"3206315495","pmid":"https://pubmed.ncbi.nlm.nih.gov/35357794"},"language":"en","primary_location":{"id":"doi:10.1515/hsz-2021-0393","doi":"https://doi.org/10.1515/hsz-2021-0393","is_oa":false,"landing_page_url":"https://doi.org/10.1515/hsz-2021-0393","pdf_url":null,"source":{"id":"https://openalex.org/S18118477","display_name":"Biological Chemistry","issn_l":"1431-6730","issn":["1431-6730","1437-4315"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-b","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310313990","host_organization_name":"De Gruyter","host_organization_lineage":["https://openalex.org/P4310313990"],"host_organization_lineage_names":["De Gruyter"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biological Chemistry","raw_type":"journal-article"},"volume":null,"type":"review","indexed_in":["arxiv","crossref","datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2110.10419","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045847201","display_name":"Gudrun Gygli","orcid":"https://orcid.org/0000-0001-9119-1778","observed_orcids":["https://orcid.org/0000-0001-9119-1778"]},"institutions":[{"id":"https://openalex.org/I102335020","display_name":"Karlsruhe Institute of Technology","ror":"https://ror.org/04t3en479","country_code":"DE","type":"education","lineage":["https://openalex.org/I102335020","https://openalex.org/I1305996414"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Gudrun Gygli","raw_affiliation_strings":["Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT) , 76344 Eggenstein-Leopoldshafen , Germany","Karlsruhe Institute of Technology"],"raw_orcid":"https://orcid.org/0000-0001-9119-1778","affiliations":[{"raw_affiliation_string":"Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT) , 76344 Eggenstein-Leopoldshafen , Germany","institution_ids":["https://openalex.org/I102335020"]},{"raw_affiliation_string":"Karlsruhe Institute of Technology","institution_ids":["https://openalex.org/I102335020"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5045847201"],"corresponding_institution_ids":["https://openalex.org/I102335020"],"apc_list":{"value":2000,"currency":"EUR","value_usd":2107},"apc_paid":null,"fwci":0.2417,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.44497608,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"403","issue":"8-9","first_page":"717","last_page":"730"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.6890000104904175,"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"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.6890000104904175,"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/T11937","display_name":"Research Data Management Practices","score":0.15410000085830688,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13539","display_name":"thermodynamics and calorimetric analyses","score":0.028999999165534973,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/enzyme-kinetics","display_name":"enzyme kinetics","score":0.9760000109672546},{"id":"https://openalex.org/keywords/reproducibility","display_name":"reproducibility","score":0.9020000100135803},{"id":"https://openalex.org/keywords/kinetic-modeling","display_name":"kinetic modeling","score":0.7360000014305115},{"id":"https://openalex.org/keywords/fair-data","display_name":"FAIR data","score":0.7820000052452087},{"id":"https://openalex.org/keywords/open-science","display_name":"open science","score":0.6769999861717224},{"id":"https://openalex.org/keywords/jupyter-notebooks","display_name":"Jupyter notebooks","score":0.7900000214576721},{"id":"https://openalex.org/keywords/python-scripting","display_name":"Python scripting","score":0.6079999804496765},{"id":"https://openalex.org/keywords/experimental-design","display_name":"experimental design","score":0.5870000123977661},{"id":"https://openalex.org/keywords/data-reporting","display_name":"data reporting","score":0.5059999823570251},{"id":"https://openalex.org/keywords/quality-control","display_name":"quality control","score":0.5540000200271606},{"id":"https://openalex.org/keywords/machine-learning","display_name":"machine learning","score":0.6340000033378601}],"concepts":[{"id":"https://openalex.org/C2780615836","wikidata":"https://www.wikidata.org/wiki/Q2471869","display_name":"USable","level":2,"score":0.7356054782867432},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.684233546257019},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6240977644920349},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.5303101539611816},{"id":"https://openalex.org/C2776548248","wikidata":"https://www.wikidata.org/wiki/Q12621536","display_name":"Judgement","level":2,"score":0.5199905037879944},{"id":"https://openalex.org/C9893847","wikidata":"https://www.wikidata.org/wiki/Q1425625","display_name":"Reproducibility","level":2,"score":0.4346396327018738},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2838771641254425},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.17323929071426392},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.12112757563591003},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.10110035538673401},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.08123108744621277},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","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}],"locations_count":6,"locations":[{"id":"doi:10.1515/hsz-2021-0393","doi":"https://doi.org/10.1515/hsz-2021-0393","is_oa":false,"landing_page_url":"https://doi.org/10.1515/hsz-2021-0393","pdf_url":null,"source":{"id":"https://openalex.org/S18118477","display_name":"Biological Chemistry","issn_l":"1431-6730","issn":["1431-6730","1437-4315"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-b","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310313990","host_organization_name":"De Gruyter","host_organization_lineage":["https://openalex.org/P4310313990"],"host_organization_lineage_names":["De Gruyter"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biological Chemistry","raw_type":"journal-article"},{"id":"pmid:35357794","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35357794","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,"listed_in":[],"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":"Biological chemistry","raw_type":"Journal Article"},{"id":"pmh:oai:arXiv.org:2110.10419","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/2110.10419","pdf_url":"https://arxiv.org/pdf/2110.10419","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"mag:3206315495","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/pdf/2110.10419","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"doi:10.48550/arxiv.2110.10419","doi":"https://doi.org/10.48550/arxiv.2110.10419","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2110.10419","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},{"id":"doi:10.15490/fairdomhub.1.investigation.483.1","doi":"https://doi.org/10.15490/fairdomhub.1.investigation.483.1","is_oa":true,"landing_page_url":"https://doi.org/10.15490/fairdomhub.1.investigation.483.1","pdf_url":null,"source":{"id":"https://openalex.org/S7407053511","display_name":"HITS gGmbH, Heidelberger Institut f\u00fcr Theoretische Studien","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I71030271","host_organization_name":"Heidelberg Institute for Theoretical Studies","host_organization_lineage":["https://openalex.org/I71030271"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Collection"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2110.10419","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/2110.10419","pdf_url":"https://arxiv.org/pdf/2110.10419","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320321990","display_name":"Ministerium f\u00fcr Wissenschaft, Forschung und Kunst Baden-W\u00fcrttemberg","ror":"https://ror.org/01hc18p32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3206315495.pdf","grobid_xml":"https://content.openalex.org/works/W3206315495.grobid-xml"},"referenced_works_count":110,"referenced_works":["https://openalex.org/W139121046","https://openalex.org/W1507935244","https://openalex.org/W1522019205","https://openalex.org/W1540384848","https://openalex.org/W1549240509","https://openalex.org/W1572384779","https://openalex.org/W1592931137","https://openalex.org/W1882735145","https://openalex.org/W1964789691","https://openalex.org/W1974141498","https://openalex.org/W1974807891","https://openalex.org/W1977502625","https://openalex.org/W1981263132","https://openalex.org/W1984498082","https://openalex.org/W1984708301","https://openalex.org/W1984802913","https://openalex.org/W2001376643","https://openalex.org/W2001771035","https://openalex.org/W2004913625","https://openalex.org/W2006224274","https://openalex.org/W2013097178","https://openalex.org/W2019726541","https://openalex.org/W2020266794","https://openalex.org/W2023099428","https://openalex.org/W2023372894","https://openalex.org/W2024568712","https://openalex.org/W2026695843","https://openalex.org/W2028928132","https://openalex.org/W2034093528","https://openalex.org/W2035832119","https://openalex.org/W2040776582","https://openalex.org/W2042721691","https://openalex.org/W2046380023","https://openalex.org/W2051834928","https://openalex.org/W2052386819","https://openalex.org/W2057246411","https://openalex.org/W2058620857","https://openalex.org/W2062537118","https://openalex.org/W2063681149","https://openalex.org/W2063731290","https://openalex.org/W2070403068","https://openalex.org/W2073870395","https://openalex.org/W2085890313","https://openalex.org/W2100837269","https://openalex.org/W2114107157","https://openalex.org/W2122961062","https://openalex.org/W2131187223","https://openalex.org/W2152335832","https://openalex.org/W2173918725","https://openalex.org/W2195266629","https://openalex.org/W2258180218","https://openalex.org/W2280989041","https://openalex.org/W2302501749","https://openalex.org/W2395099523","https://openalex.org/W2403087393","https://openalex.org/W2406493898","https://openalex.org/W2418050666","https://openalex.org/W2428655024","https://openalex.org/W2481300999","https://openalex.org/W2499815005","https://openalex.org/W2528491735","https://openalex.org/W2548956425","https://openalex.org/W2558342853","https://openalex.org/W2559481386","https://openalex.org/W2570342360","https://openalex.org/W2582546513","https://openalex.org/W2594475271","https://openalex.org/W2624613947","https://openalex.org/W2751743037","https://openalex.org/W2761107667","https://openalex.org/W2781968731","https://openalex.org/W2783983658","https://openalex.org/W2789816182","https://openalex.org/W2802978240","https://openalex.org/W2888636847","https://openalex.org/W2892160779","https://openalex.org/W2894803669","https://openalex.org/W2920400247","https://openalex.org/W2922470285","https://openalex.org/W2925580016","https://openalex.org/W2938803199","https://openalex.org/W2949836779","https://openalex.org/W2952789681","https://openalex.org/W2971454236","https://openalex.org/W2973929545","https://openalex.org/W2995106228","https://openalex.org/W3005067728","https://openalex.org/W3023839943","https://openalex.org/W3029881688","https://openalex.org/W3034479940","https://openalex.org/W3035847987","https://openalex.org/W3047705479","https://openalex.org/W3081286783","https://openalex.org/W3082396276","https://openalex.org/W3083563065","https://openalex.org/W3092019244","https://openalex.org/W3094845984","https://openalex.org/W3130181623","https://openalex.org/W3130828674","https://openalex.org/W3134818558","https://openalex.org/W3148019492","https://openalex.org/W3160630894","https://openalex.org/W3187630243","https://openalex.org/W3198351703","https://openalex.org/W4206117801","https://openalex.org/W4210980745","https://openalex.org/W4235243453","https://openalex.org/W4247909164","https://openalex.org/W4253172274","https://openalex.org/W6943650601"],"related_works":["https://openalex.org/W4319826358","https://openalex.org/W6962787059","https://openalex.org/W3186459508","https://openalex.org/W4402858723","https://openalex.org/W7207623763","https://openalex.org/W2104556779","https://openalex.org/W4395031525","https://openalex.org/W7099055441","https://openalex.org/W4411207382","https://openalex.org/W2136033007"],"abstract_inverted_index":{"Enzyme":[0],"reactions":[1],"are":[2,118,126,141],"highly":[3],"dependent":[4],"on":[5],"reaction":[6,13,33,57,95,157],"conditions.":[7],"To":[8],"ensure":[9],"reproducibility":[10],"of":[11,31,93,105,109,133,155],"enzyme":[12,32,56,94,111,156],"parameters,":[14,34],"experiments":[15,89],"need":[16,47],"to":[17,27,48,85,144],"be":[18,49,60],"carefully":[19],"designed":[20],"and":[21,62,73,80,97,102,116,125,137,152],"kinetic":[22,107],"modeling":[23,39,108],"meticulously":[24],"executed.":[25],"Furthermore,":[26],"enable":[28],"quality":[29],"control":[30],"the":[35,38,44,91,106,114,131,149],"experimental":[36],"conditions,":[37],"process":[40],"as":[41,43,68,70],"well":[42,69],"raw":[45],"data":[46,135],"reported":[50],"comprehensively.":[51],"By":[52],"taking":[53],"these":[54,78],"steps,":[55],"parameters":[58,96],"can":[59],"open":[61,151],"FAIR":[63,101,153],"(findable,":[64],"accessible,":[65],"interoperable,":[66],"re-usable)":[67],"repeatable,":[71],"replicable":[72],"reproducible.":[74],"This":[75],"review":[76],"discusses":[77],"requirements":[79],"provides":[81],"a":[82],"practical":[83],"guide":[84,115],"designing":[86],"initial":[87],"rate":[88],"for":[90,148],"determination":[92],"gives":[98],"an":[99,110],"open,":[100],"re-editable":[103],"example":[104,117],"reaction.":[112],"Both":[113],"scripted":[119],"with":[120],"Python":[121],"in":[122],"Jupyter":[123],"Notebooks":[124],"publicly":[127],"available":[128],"(https://fairdomhub.org/investigations/483/snapshots/1).":[129],"Finally,":[130],"prerequisites":[132],"automated":[134],"analysis":[136],"machine":[138],"learning":[139],"algorithms":[140],"briefly":[142],"discussed":[143],"provide":[145],"further":[146],"motivation":[147],"comprehensive,":[150],"reporting":[154],"parameters.":[158]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2021-10-25T00:00:00"}
