{"id":"https://openalex.org/W2140344793","doi":"https://doi.org/10.1186/1471-2105-10-199","title":"DOTcvpSB, a software toolbox for dynamic optimization in systems biology","display_name":"DOTcvpSB, a software toolbox for dynamic optimization in systems biology","publication_year":2009,"publication_date":"2009-06-29","ids":{"openalex":"https://openalex.org/W2140344793","doi":"https://doi.org/10.1186/1471-2105-10-199","mag":"2140344793","pmid":"https://pubmed.ncbi.nlm.nih.gov/19558728"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-199","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-199","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-199","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-199","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111639746","display_name":"T. Hirmajer","orcid":null},"institutions":[{"id":"https://openalex.org/I4210145572","display_name":"Institute of Neuroimmunology of the Slovak Academy of Sciences","ror":"https://ror.org/05c516317","country_code":"SK","type":"facility","lineage":["https://openalex.org/I207624831","https://openalex.org/I4210145572"]},{"id":"https://openalex.org/I4210101760","display_name":"Instituto de Investigaci\u00f3ns Mari\u00f1as","ror":"https://ror.org/01603fg59","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210101760"]},{"id":"https://openalex.org/I134820265","display_name":"Consejo Superior de Investigaciones Cient\u00edficas","ror":"https://ror.org/02gfc7t72","country_code":"ES","type":"funder","lineage":["https://openalex.org/I134820265"]},{"id":"https://openalex.org/I207624831","display_name":"Slovak Academy of Sciences","ror":"https://ror.org/03h7qq074","country_code":"SK","type":"funder","lineage":["https://openalex.org/I207624831"]}],"countries":["ES","SK"],"is_corresponding":true,"raw_author_name":"Tom\u00e1\u0161 Hirmajer","raw_affiliation_strings":["Instituto de Investigaciones Marinas, IIM-CSIC, Spanish Council for Scientific Research, C/Eduardo Cabello 6, 36208 Vigo, Spain. thirmajer@gmail.com","Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic","Instituto de Investigaciones Marinas, IIM-CSIC, Spanish Council for Scientific Research, Vigo, Spain"],"affiliations":[{"raw_affiliation_string":"Instituto de Investigaciones Marinas, IIM-CSIC, Spanish Council for Scientific Research, C/Eduardo Cabello 6, 36208 Vigo, Spain. thirmajer@gmail.com","institution_ids":["https://openalex.org/I4210101760"]},{"raw_affiliation_string":"Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic","institution_ids":["https://openalex.org/I207624831","https://openalex.org/I4210145572"]},{"raw_affiliation_string":"Instituto de Investigaciones Marinas, IIM-CSIC, Spanish Council for Scientific Research, Vigo, Spain","institution_ids":["https://openalex.org/I134820265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058138681","display_name":"Eva Balsa\u2010Canto","orcid":"https://orcid.org/0000-0002-1978-2626"},"institutions":[{"id":"https://openalex.org/I134820265","display_name":"Consejo Superior de Investigaciones Cient\u00edficas","ror":"https://ror.org/02gfc7t72","country_code":"ES","type":"funder","lineage":["https://openalex.org/I134820265"]},{"id":"https://openalex.org/I4210101760","display_name":"Instituto de Investigaci\u00f3ns Mari\u00f1as","ror":"https://ror.org/01603fg59","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210101760"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Eva Balsa-Canto","raw_affiliation_strings":["Instituto de Investigaciones Marinas, IIM-CSIC, Spanish Council for Scientific Research, C/Eduardo Cabello 6, 36208, Vigo, Spain","Instituto de Investigaciones Marinas, IIM-CSIC, Spanish Council for Scientific Research, Vigo, Spain"],"affiliations":[{"raw_affiliation_string":"Instituto de Investigaciones Marinas, IIM-CSIC, Spanish Council for Scientific Research, C/Eduardo Cabello 6, 36208, Vigo, Spain","institution_ids":["https://openalex.org/I4210101760"]},{"raw_affiliation_string":"Instituto de Investigaciones Marinas, IIM-CSIC, Spanish Council for Scientific Research, Vigo, Spain","institution_ids":["https://openalex.org/I134820265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090264675","display_name":"Julio R. Banga","orcid":"https://orcid.org/0000-0002-4245-0320"},"institutions":[{"id":"https://openalex.org/I4210101760","display_name":"Instituto de Investigaci\u00f3ns Mari\u00f1as","ror":"https://ror.org/01603fg59","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210101760"]},{"id":"https://openalex.org/I134820265","display_name":"Consejo Superior de Investigaciones Cient\u00edficas","ror":"https://ror.org/02gfc7t72","country_code":"ES","type":"funder","lineage":["https://openalex.org/I134820265"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Julio R Banga","raw_affiliation_strings":["Instituto de Investigaciones Marinas, IIM-CSIC, Spanish Council for Scientific Research, C/Eduardo Cabello 6, 36208, Vigo, Spain","Instituto de Investigaciones Marinas, IIM-CSIC, Spanish Council for Scientific Research, Vigo, Spain"],"affiliations":[{"raw_affiliation_string":"Instituto de Investigaciones Marinas, IIM-CSIC, Spanish Council for Scientific Research, C/Eduardo Cabello 6, 36208, Vigo, Spain","institution_ids":["https://openalex.org/I4210101760"]},{"raw_affiliation_string":"Instituto de Investigaciones Marinas, IIM-CSIC, Spanish Council for Scientific Research, Vigo, Spain","institution_ids":["https://openalex.org/I134820265"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5111639746"],"corresponding_institution_ids":["https://openalex.org/I134820265","https://openalex.org/I207624831","https://openalex.org/I4210101760","https://openalex.org/I4210145572"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.4171,"has_fulltext":true,"cited_by_count":50,"citation_normalized_percentile":{"value":0.89028414,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"10","issue":"1","first_page":"199","last_page":"199"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9980000257492065,"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":0.9916999936103821,"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":0.7249138355255127},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.7135920524597168},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.6758688688278198},{"id":"https://openalex.org/keywords/optimization-problem","display_name":"Optimization problem","score":0.5460283160209656},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5220887064933777},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.4199722409248352},{"id":"https://openalex.org/keywords/continuous-optimization","display_name":"Continuous optimization","score":0.41418203711509705},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.41406774520874023},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.15319204330444336},{"id":"https://openalex.org/keywords/multi-swarm-optimization","display_name":"Multi-swarm optimization","score":0.14775824546813965},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10974809527397156},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10448399186134338}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7249138355255127},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.7135920524597168},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.6758688688278198},{"id":"https://openalex.org/C137836250","wikidata":"https://www.wikidata.org/wiki/Q984063","display_name":"Optimization problem","level":2,"score":0.5460283160209656},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5220887064933777},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.4199722409248352},{"id":"https://openalex.org/C92995354","wikidata":"https://www.wikidata.org/wiki/Q5165499","display_name":"Continuous optimization","level":4,"score":0.41418203711509705},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.41406774520874023},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.15319204330444336},{"id":"https://openalex.org/C122357587","wikidata":"https://www.wikidata.org/wiki/Q6934508","display_name":"Multi-swarm optimization","level":3,"score":0.14775824546813965},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10974809527397156},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10448399186134338},{"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/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.0},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.0}],"mesh":[{"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":"D016208","descriptor_name":"Databases, Factual","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":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"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":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-10-199","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-199","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-199","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19558728","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19558728","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:digital.csic.es:10261/17430","is_oa":false,"landing_page_url":"http://hdl.handle.net/10261/17430","pdf_url":null,"source":{"id":"https://openalex.org/S4306400616","display_name":"DIGITAL.CSIC (Spanish National Research Council (CSIC))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I134820265","host_organization_name":"Consejo Superior de Investigaciones Cient\u00edficas","host_organization_lineage":["https://openalex.org/I134820265"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"art\u00edculo"},{"id":"pmh:oai:doaj.org/article:f34162800f714dad8ed295456befaab4","is_oa":true,"landing_page_url":"https://doaj.org/article/f34162800f714dad8ed295456befaab4","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 10, Iss 1, p 199 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2717952","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2717952","pdf_url":null,"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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-199","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-199","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-199","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":"https://ror.org/034900433"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2140344793.pdf","grobid_xml":"https://content.openalex.org/works/W2140344793.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1595159159","https://openalex.org/W1970565927","https://openalex.org/W1982258483","https://openalex.org/W1996195324","https://openalex.org/W2007591867","https://openalex.org/W2008779528","https://openalex.org/W2018409816","https://openalex.org/W2023177201","https://openalex.org/W2028715997","https://openalex.org/W2033837064","https://openalex.org/W2070425465","https://openalex.org/W2093414411","https://openalex.org/W2098740506","https://openalex.org/W2102653059","https://openalex.org/W2105363557","https://openalex.org/W2111442058","https://openalex.org/W2115343689","https://openalex.org/W2123871098","https://openalex.org/W2129935828","https://openalex.org/W2137128504","https://openalex.org/W2139869608","https://openalex.org/W2150908245","https://openalex.org/W2151339633","https://openalex.org/W2151833886","https://openalex.org/W2157556374","https://openalex.org/W2166071821","https://openalex.org/W2166751342","https://openalex.org/W2547101588","https://openalex.org/W2972681909","https://openalex.org/W3136837693"],"related_works":["https://openalex.org/W3200088983","https://openalex.org/W2243008534","https://openalex.org/W2561596083","https://openalex.org/W3161088745","https://openalex.org/W339959573","https://openalex.org/W135428843","https://openalex.org/W2948527927","https://openalex.org/W2135196975","https://openalex.org/W2990762041","https://openalex.org/W2353523849"],"abstract_inverted_index":{"Here":[0],"we":[1],"illustrate":[2,33],"the":[3,26,35,41],"capabilities":[4],"and":[5,25],"performance":[6],"of":[7,28,37,44,48],"DOTcvpSB":[8],"by":[9],"solving":[10],"several":[11],"challenging":[12,53],"optimization":[13,50],"problems":[14],"related":[15],"with":[16],"bioreactor":[17],"optimization,":[18],"optimal":[19],"drug":[20],"infusion":[21],"to":[22],"a":[23,45],"patient":[24],"minimization":[27],"intracellular":[29],"oscillations.":[30],"The":[31,56],"results":[32],"how":[34],"suite":[36],"solvers":[38],"available":[39,60],"allows":[40],"efficient":[42],"solution":[43],"wide":[46],"class":[47],"dynamic":[49],"problems,":[51],"including":[52],"multimodal":[54],"ones.":[55],"toolbox":[57],"is":[58],"freely":[59],"for":[61],"academic":[62],"use.":[63]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":5}],"updated_date":"2026-03-18T14:38:29.013473","created_date":"2025-10-10T00:00:00"}
