{"id":"https://openalex.org/W4389504912","doi":"https://doi.org/10.1093/bioinformatics/btad745","title":"CytoCopasi: a chemical systems biology target and drug discovery visual data analytics platform","display_name":"CytoCopasi: a chemical systems biology target and drug discovery visual data analytics platform","publication_year":2023,"publication_date":"2023-12-01","ids":{"openalex":"https://openalex.org/W4389504912","doi":"https://doi.org/10.1093/bioinformatics/btad745","pmid":"https://pubmed.ncbi.nlm.nih.gov/38070155"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad745","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad745","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad745/54182403/btad745.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad745/54182403/btad745.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085642534","display_name":"Hikmet Emre Kaya","orcid":null},"institutions":[{"id":"https://openalex.org/I157614274","display_name":"University of Cape Town","ror":"https://ror.org/03p74gp79","country_code":"ZA","type":"education","lineage":["https://openalex.org/I157614274"]}],"countries":["ZA"],"is_corresponding":true,"raw_author_name":"Hikmet Emre Kaya","raw_affiliation_strings":["Department of Chemistry, Scientific Computing Research Unit, PD Hahn Building, University of Cape Town , Rondebosch 7701, South Africa","Department of Chemistry, PD Hahn Building, University of Cape Town, Rondebosch, 7701"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Scientific Computing Research Unit, PD Hahn Building, University of Cape Town , Rondebosch 7701, South Africa","institution_ids":["https://openalex.org/I157614274"]},{"raw_affiliation_string":"Department of Chemistry, PD Hahn Building, University of Cape Town, Rondebosch, 7701","institution_ids":["https://openalex.org/I157614274"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006872896","display_name":"Kevin J. Naidoo","orcid":"https://orcid.org/0000-0002-9898-3708"},"institutions":[{"id":"https://openalex.org/I157614274","display_name":"University of Cape Town","ror":"https://ror.org/03p74gp79","country_code":"ZA","type":"education","lineage":["https://openalex.org/I157614274"]}],"countries":["ZA"],"is_corresponding":false,"raw_author_name":"Kevin J Naidoo","raw_affiliation_strings":["Department of Chemistry, Scientific Computing Research Unit, PD Hahn Building, University of Cape Town , Rondebosch 7701, South Africa","Department of Chemistry, PD Hahn Building, University of Cape Town, Rondebosch, 7701"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Scientific Computing Research Unit, PD Hahn Building, University of Cape Town , Rondebosch 7701, South Africa","institution_ids":["https://openalex.org/I157614274"]},{"raw_affiliation_string":"Department of Chemistry, PD Hahn Building, University of Cape Town, Rondebosch, 7701","institution_ids":["https://openalex.org/I157614274"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5085642534"],"corresponding_institution_ids":["https://openalex.org/I157614274"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7613,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.7380033,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"39","issue":"12","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9993000030517578,"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":0.9993000030517578,"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":0.9991000294685364,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7838315963745117},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.7193522453308105},{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.7050033807754517},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.5231112837791443},{"id":"https://openalex.org/keywords/analytics","display_name":"Analytics","score":0.5226568579673767},{"id":"https://openalex.org/keywords/visual-analytics","display_name":"Visual analytics","score":0.5135624408721924},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4701017737388611},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.45861271023750305},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4500636160373688},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.4485829174518585},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.41245758533477783},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37414711713790894},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2663626968860626},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.19308096170425415},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.18470200896263123},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.15402552485466003},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14347189664840698},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08960863947868347}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7838315963745117},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7193522453308105},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.7050033807754517},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.5231112837791443},{"id":"https://openalex.org/C79158427","wikidata":"https://www.wikidata.org/wiki/Q485396","display_name":"Analytics","level":2,"score":0.5226568579673767},{"id":"https://openalex.org/C59732488","wikidata":"https://www.wikidata.org/wiki/Q2528440","display_name":"Visual analytics","level":3,"score":0.5135624408721924},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4701017737388611},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.45861271023750305},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4500636160373688},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.4485829174518585},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.41245758533477783},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37414711713790894},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2663626968860626},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.19308096170425415},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.18470200896263123},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.15402552485466003},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14347189664840698},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08960863947868347}],"mesh":[{"descriptor_ui":"D000077488","descriptor_name":"Data Science","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077488","descriptor_name":"Data Science","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077488","descriptor_name":"Data Science","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077488","descriptor_name":"Data Science","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077488","descriptor_name":"Data Science","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077488","descriptor_name":"Data Science","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":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad745","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad745","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad745/54182403/btad745.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:38070155","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38070155","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:10963058","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10963058","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10963058/pdf/btad745.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad745","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad745","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad745/54182403/btad745.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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/G3034753964","display_name":null,"funder_award_id":"grant","funder_id":"https://openalex.org/F4320320671","funder_display_name":"National Research Foundation"},{"id":"https://openalex.org/G4165398850","display_name":null,"funder_award_id":"CPPR 466624","funder_id":"https://openalex.org/F4320320671","funder_display_name":"National Research Foundation"}],"funders":[{"id":"https://openalex.org/F4320317425","display_name":"Dane O. Kildsig Center for Pharmaceutical Processing Research","ror":null},{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320320672","display_name":"South African Medical Research Council","ror":"https://ror.org/05q60vz69"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4389504912.pdf"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1820499699","https://openalex.org/W1968467027","https://openalex.org/W1989263028","https://openalex.org/W1999840377","https://openalex.org/W2015502339","https://openalex.org/W2016710415","https://openalex.org/W2041935553","https://openalex.org/W2043696829","https://openalex.org/W2044935306","https://openalex.org/W2051959027","https://openalex.org/W2059581116","https://openalex.org/W2072996759","https://openalex.org/W2097508475","https://openalex.org/W2097744318","https://openalex.org/W2102653059","https://openalex.org/W2107062718","https://openalex.org/W2117364474","https://openalex.org/W2138326194","https://openalex.org/W2146737319","https://openalex.org/W2150908245","https://openalex.org/W2158590514","https://openalex.org/W2159482845","https://openalex.org/W2159628188","https://openalex.org/W2159675211","https://openalex.org/W2167301307","https://openalex.org/W2213280398","https://openalex.org/W2597995360","https://openalex.org/W2767557279","https://openalex.org/W2888577663","https://openalex.org/W2903072518","https://openalex.org/W3201715663","https://openalex.org/W4252988319","https://openalex.org/W4255600944","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W2138326194","https://openalex.org/W4385891864","https://openalex.org/W2150908245","https://openalex.org/W4321472021","https://openalex.org/W2136043941","https://openalex.org/W2097410126","https://openalex.org/W2211443823","https://openalex.org/W2043776573","https://openalex.org/W2735157934","https://openalex.org/W2026725606"],"abstract_inverted_index":{"The":[0],"COPASI":[1],"files,":[2],"simulation":[3],"data,":[4],"native":[5],"libraries,":[6],"and":[7],"the":[8],"manual":[9],"are":[10],"available":[11],"on":[12],"https://github.com/scientificomputing/CytoCopasi.":[13]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
