{"id":"https://openalex.org/W2793858867","doi":"https://doi.org/10.1093/bioinformatics/bty089","title":"ShinyKGode: an interactive application for ODE parameter inference using gradient matching","display_name":"ShinyKGode: an interactive application for ODE parameter inference using gradient matching","publication_year":2018,"publication_date":"2018-02-26","ids":{"openalex":"https://openalex.org/W2793858867","doi":"https://doi.org/10.1093/bioinformatics/bty089","mag":"2793858867","pmid":"https://pubmed.ncbi.nlm.nih.gov/29490021"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty089","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty089","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/2314/25098612/bty089.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/34/13/2314/25098612/bty089.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034049617","display_name":"Joe Wandy","orcid":"https://orcid.org/0000-0002-3068-4664"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Joe Wandy","raw_affiliation_strings":["Glasgow Polyomics, University of Glasgow, Glasgow, UK"],"affiliations":[{"raw_affiliation_string":"Glasgow Polyomics, University of Glasgow, Glasgow, UK","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089799265","display_name":"Mu Niu","orcid":"https://orcid.org/0000-0002-3068-5501"},"institutions":[{"id":"https://openalex.org/I897542642","display_name":"University of Plymouth","ror":"https://ror.org/008n7pv89","country_code":"GB","type":"education","lineage":["https://openalex.org/I897542642"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mu Niu","raw_affiliation_strings":["School of Computing, Electronics and Mathematics, University of Plymouth, Devon, UK"],"affiliations":[{"raw_affiliation_string":"School of Computing, Electronics and Mathematics, University of Plymouth, Devon, UK","institution_ids":["https://openalex.org/I897542642"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011531658","display_name":"Diana Giurghita","orcid":"https://orcid.org/0000-0002-5725-4162"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Diana Giurghita","raw_affiliation_strings":["School of Mathematics and Statistics, University of Glasgow, Glasgow, UK"],"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, University of Glasgow, Glasgow, UK","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043557336","display_name":"R\u00f3n\u00e1n Daly","orcid":"https://orcid.org/0000-0002-1275-6820"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"R\u00f3n\u00e1n Daly","raw_affiliation_strings":["Glasgow Polyomics, University of Glasgow, Glasgow, UK"],"affiliations":[{"raw_affiliation_string":"Glasgow Polyomics, University of Glasgow, Glasgow, UK","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060432668","display_name":"Simon Rogers","orcid":"https://orcid.org/0000-0003-3578-4477"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Simon Rogers","raw_affiliation_strings":["School of Computing Science, University of Glasgow, Glasgow, UK"],"affiliations":[{"raw_affiliation_string":"School of Computing Science, University of Glasgow, Glasgow, UK","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080836461","display_name":"Dirk Husmeier","orcid":"https://orcid.org/0000-0003-1673-7413"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Dirk Husmeier","raw_affiliation_strings":["School of Mathematics and Statistics, University of Glasgow, Glasgow, UK"],"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, University of Glasgow, Glasgow, UK","institution_ids":["https://openalex.org/I7882870"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5034049617"],"corresponding_institution_ids":["https://openalex.org/I7882870"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":1028,"currency":"EUR","value_usd":1108},"fwci":0.0927,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.46332184,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"34","issue":"13","first_page":"2314","last_page":"2315"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9980999827384949,"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":0.9980999827384949,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9955999851226807,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9854000210762024,"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/ode","display_name":"Ode","score":0.9246302247047424},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.8301407098770142},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7356482744216919},{"id":"https://openalex.org/keywords/ordinary-differential-equation","display_name":"Ordinary differential equation","score":0.6675469279289246},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6441122889518738},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6267501711845398},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.5388597249984741},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.48536837100982666},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4540449380874634},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4538697600364685},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.442352294921875},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3913898169994354},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.38805603981018066},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.25460362434387207},{"id":"https://openalex.org/keywords/differential-equation","display_name":"Differential equation","score":0.23639675974845886},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2294718325138092},{"id":"https://openalex.org/keywords/applied-mathematics","display_name":"Applied mathematics","score":0.20218893885612488},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16133224964141846},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.14670348167419434}],"concepts":[{"id":"https://openalex.org/C34862557","wikidata":"https://www.wikidata.org/wiki/Q178985","display_name":"Ode","level":2,"score":0.9246302247047424},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.8301407098770142},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7356482744216919},{"id":"https://openalex.org/C51544822","wikidata":"https://www.wikidata.org/wiki/Q465274","display_name":"Ordinary differential equation","level":3,"score":0.6675469279289246},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6441122889518738},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6267501711845398},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.5388597249984741},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.48536837100982666},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4540449380874634},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4538697600364685},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.442352294921875},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3913898169994354},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.38805603981018066},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.25460362434387207},{"id":"https://openalex.org/C78045399","wikidata":"https://www.wikidata.org/wiki/Q11214","display_name":"Differential equation","level":2,"score":0.23639675974845886},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2294718325138092},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.20218893885612488},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16133224964141846},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.14670348167419434},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"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":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/bty089","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty089","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/2314/25098612/bty089.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:29490021","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29490021","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:eprints.gla.ac.uk:157270","is_oa":true,"landing_page_url":"http://eprints.gla.ac.uk/view/author/36328.html>","pdf_url":null,"source":{"id":"https://openalex.org/S4210235606","display_name":"ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam)","issn_l":"2622-8912","issn":["2622-8912","2622-8920"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"},{"id":"pmh:oai:europepmc.org:4991148","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6022662","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"pmh:oai:pearl.plymouth.ac.uk:10026.1/17958","is_oa":false,"landing_page_url":"http://hdl.handle.net/10026.1/17958","pdf_url":null,"source":{"id":"https://openalex.org/S4306402507","display_name":"PEARL (University of Plymouth)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I897542642","host_organization_name":"University of Plymouth","host_organization_lineage":["https://openalex.org/I897542642"],"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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty089","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty089","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/2314/25098612/bty089.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/G1190157208","display_name":null,"funder_award_id":"EP/L020319/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G3071701163","display_name":"Computational inference of biopathway dynamics and structures","funder_award_id":"EP/L020319/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G6613322278","display_name":null,"funder_award_id":"105614/Z/14/Z","funder_id":"https://openalex.org/F4320307874","funder_display_name":"Wellcome"}],"funders":[{"id":"https://openalex.org/F4320307874","display_name":"Wellcome","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2793858867.pdf","grobid_xml":"https://content.openalex.org/works/W2793858867.grobid-xml"},"referenced_works_count":5,"referenced_works":["https://openalex.org/W2169264416","https://openalex.org/W2460801207","https://openalex.org/W2742379511","https://openalex.org/W6719161671","https://openalex.org/W6741992186"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2150908245","https://openalex.org/W2981332207","https://openalex.org/W2159912904","https://openalex.org/W2211443823","https://openalex.org/W2100525485","https://openalex.org/W2040642413","https://openalex.org/W3048335229","https://openalex.org/W2146744007","https://openalex.org/W2890725831"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}