{"id":"https://openalex.org/W2091708614","doi":"https://doi.org/10.1186/1471-2105-11-455","title":"Next generation tools for genomic data generation, distribution, and visualization","display_name":"Next generation tools for genomic data generation, distribution, and visualization","publication_year":2010,"publication_date":"2010-09-01","ids":{"openalex":"https://openalex.org/W2091708614","doi":"https://doi.org/10.1186/1471-2105-11-455","mag":"2091708614"},"language":"en","primary_location":{"id":"pmh:oai:doaj.org/article:8319cf5588fd4739a512306c7dace498","is_oa":false,"landing_page_url":"https://doaj.org/article/8319cf5588fd4739a512306c7dace498","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 11, Iss 1, p 455 (2010)","raw_type":"article"},"type":"article","indexed_in":["doaj"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050013277","display_name":"David A. Nix","orcid":"https://orcid.org/0009-0002-3383-8582"},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]},{"id":"https://openalex.org/I2801159745","display_name":"Huntsman Cancer Institute","ror":"https://ror.org/03v7tx966","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801159745","https://openalex.org/I4210148268"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nix David A","raw_affiliation_strings":["Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, USA","institution_ids":["https://openalex.org/I2801159745","https://openalex.org/I223532165"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044324792","display_name":"Tonya L Di Sera","orcid":null},"institutions":[{"id":"https://openalex.org/I2801159745","display_name":"Huntsman Cancer Institute","ror":"https://ror.org/03v7tx966","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801159745","https://openalex.org/I4210148268"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Di Sera Tonya L","raw_affiliation_strings":["Research Informatics, Huntsman Cancer Institute, Salt Lake City, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Informatics, Huntsman Cancer Institute, Salt Lake City, USA","institution_ids":["https://openalex.org/I2801159745"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040165546","display_name":"Brian K. Dalley","orcid":"https://orcid.org/0009-0003-9774-5200"},"institutions":[{"id":"https://openalex.org/I2801159745","display_name":"Huntsman Cancer Institute","ror":"https://ror.org/03v7tx966","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801159745","https://openalex.org/I4210148268"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dalley Brian K","raw_affiliation_strings":["Microarray/Next Generation Sequencing Shared Resource, Huntsman Cancer Institute, Salt Lake City, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Microarray/Next Generation Sequencing Shared Resource, Huntsman Cancer Institute, Salt Lake City, USA","institution_ids":["https://openalex.org/I2801159745"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015615781","display_name":"Brett Milash","orcid":null},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]},{"id":"https://openalex.org/I2801159745","display_name":"Huntsman Cancer Institute","ror":"https://ror.org/03v7tx966","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801159745","https://openalex.org/I4210148268"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Milash Brett A","raw_affiliation_strings":["Bioinformatics Shared Resource, University of Utah, Huntsman Cancer Institute, Salt Lake City, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Shared Resource, University of Utah, Huntsman Cancer Institute, Salt Lake City, USA","institution_ids":["https://openalex.org/I2801159745","https://openalex.org/I223532165"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004450794","display_name":"Robert M Cundick","orcid":null},"institutions":[{"id":"https://openalex.org/I2801159745","display_name":"Huntsman Cancer Institute","ror":"https://ror.org/03v7tx966","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801159745","https://openalex.org/I4210148268"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cundick Robert M","raw_affiliation_strings":["Research Informatics, Huntsman Cancer Institute, Salt Lake City, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Informatics, Huntsman Cancer Institute, Salt Lake City, USA","institution_ids":["https://openalex.org/I2801159745"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060364183","display_name":"Kevin S Quinn","orcid":null},"institutions":[{"id":"https://openalex.org/I2801159745","display_name":"Huntsman Cancer Institute","ror":"https://ror.org/03v7tx966","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801159745","https://openalex.org/I4210148268"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Quinn Kevin S","raw_affiliation_strings":["Research Informatics, Huntsman Cancer Institute, Salt Lake City, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Informatics, Huntsman Cancer Institute, Salt Lake City, USA","institution_ids":["https://openalex.org/I2801159745"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006767999","display_name":"Samir Courdy","orcid":null},"institutions":[{"id":"https://openalex.org/I2801159745","display_name":"Huntsman Cancer Institute","ror":"https://ror.org/03v7tx966","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801159745","https://openalex.org/I4210148268"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Courdy Samir J","raw_affiliation_strings":["Research Informatics, Huntsman Cancer Institute, Salt Lake City, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Informatics, Huntsman Cancer Institute, Salt Lake City, USA","institution_ids":["https://openalex.org/I2801159745"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5050013277"],"corresponding_institution_ids":["https://openalex.org/I223532165","https://openalex.org/I2801159745"],"apc_list":null,"apc_paid":null,"fwci":1.9063,"has_fulltext":true,"cited_by_count":47,"citation_normalized_percentile":{"value":0.85352956,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9950000047683716,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9950000047683716,"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":0.9897000193595886,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9846000075340271,"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":0.7136370539665222},{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.6122276782989502},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.5471028089523315},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.4949762225151062},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.47587504982948303},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.47179049253463745},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4466648995876312},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.4454256594181061},{"id":"https://openalex.org/keywords/big-data","display_name":"Big data","score":0.412663072347641},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4068465828895569},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.30713149905204773},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.22786813974380493},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.19697532057762146},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.16445395350456238},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11896693706512451}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7136370539665222},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.6122276782989502},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.5471028089523315},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.4949762225151062},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.47587504982948303},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.47179049253463745},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4466648995876312},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.4454256594181061},{"id":"https://openalex.org/C75684735","wikidata":"https://www.wikidata.org/wiki/Q858810","display_name":"Big data","level":2,"score":0.412663072347641},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4068465828895569},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.30713149905204773},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.22786813974380493},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.19697532057762146},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.16445395350456238},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11896693706512451},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"pmh:oai:doaj.org/article:8319cf5588fd4739a512306c7dace498","is_oa":false,"landing_page_url":"https://doaj.org/article/8319cf5588fd4739a512306c7dace498","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 11, Iss 1, p 455 (2010)","raw_type":"article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.5299999713897705}],"awards":[{"id":"https://openalex.org/G5547772573","display_name":null,"funder_award_id":"P01CA24014","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1488086388","https://openalex.org/W1583240815","https://openalex.org/W1977859620","https://openalex.org/W2015416439","https://openalex.org/W2017840637","https://openalex.org/W2026662234","https://openalex.org/W2072229457","https://openalex.org/W2092387193","https://openalex.org/W2127640118","https://openalex.org/W2144303444","https://openalex.org/W2145477956","https://openalex.org/W2152710395","https://openalex.org/W2154519319","https://openalex.org/W2158304452","https://openalex.org/W2160379721","https://openalex.org/W2916408032"],"related_works":["https://openalex.org/W1657880117","https://openalex.org/W2595172197","https://openalex.org/W2127970246","https://openalex.org/W2084856301","https://openalex.org/W1001352512","https://openalex.org/W4382618745","https://openalex.org/W2885125400","https://openalex.org/W1989889224","https://openalex.org/W2748922771","https://openalex.org/W1987128138"],"abstract_inverted_index":{"Abstract":[0],"Background":[1],"With":[2],"the":[3,16,24,80,116,175],"rapidly":[4],"falling":[5],"cost":[6],"and":[7,13,26,36,54,65,74,88,113,128,148,192,194,204],"availability":[8],"of":[9,32,146],"high":[10],"throughput":[11],"sequencing":[12],"microarray":[14],"technologies,":[15],"bottleneck":[17],"for":[18,50,72,198],"effectively":[19,33],"using":[20,79],"genomic":[21,38,56,77,159],"analysis":[22,66,101],"in":[23,186],"laboratory":[25],"clinic":[27],"is":[28],"shifting":[29],"to":[30,104,123],"one":[31],"managing,":[34],"analyzing,":[35,52],"sharing":[37],"data.":[39,57],"Results":[40],"Here":[41],"we":[42],"present":[43],"three":[44],"open-source,":[45],"platform":[46],"independent,":[47],"software":[48],"tools":[49,102,181],"generating,":[51],"distributing,":[53],"visualizing":[55],"These":[58,180],"include":[59],"a":[60,89,129,133,138],"next":[61],"generation":[62],"sequencing/microarray":[63],"LIMS":[64],"project":[67],"center":[68],"(GNomEx);":[69],"an":[70],"application":[71,93],"annotating":[73],"programmatically":[75,168],"distributing":[76],"data":[78,84,150,160],"community":[81],"vetted":[82],"DAS/2":[83],"exchange":[85],"protocol":[86],"(GenoPub);":[87],"standalone":[90],"Java":[91,126],"Swing":[92],"(GWrap)":[94],"that":[95,162],"makes":[96],"cutting":[97],"edge":[98],"command":[99],"line":[100],"available":[103,197],"those":[105],"who":[106],"prefer":[107],"graphical":[108],"user":[109],"interfaces.":[110],"Both":[111,136],"GNomEx":[112],"GenoPub":[114],"use":[115,185],"rich":[117],"client":[118,171],"Flex/Flash":[119],"web":[120],"browser":[121],"interface":[122],"interact":[124],"with":[125],"classes":[127],"relational":[130],"database":[131],"on":[132],"remote":[134],"server.":[135],"employ":[137],"public-private":[139],"user-group":[140],"security":[141],"model":[142],"enabling":[143],"controlled":[144],"distribution":[145],"patient":[147],"unpublished":[149],"alongside":[151],"public":[152],"resources.":[153],"As":[154],"such,":[155],"they":[156],"function":[157],"as":[158,174],"repositories":[161],"can":[163],"be":[164],"accessed":[165],"manually":[166],"or":[167],"through":[169],"DAS/2-enabled":[170],"applications":[172],"such":[173],"Integrated":[176],"Genome":[177],"Browser.":[178],"Conclusions":[179],"have":[182],"gained":[183],"wide":[184],"our":[187],"core":[188],"facilities,":[189],"research":[190],"laboratories":[191],"clinics":[193],"are":[195],"freely":[196],"non-profit":[199],"use.":[200],"See":[201],"<url>http://sourceforge.net/projects/gnomex/</url>,":[202],"<url>http://sourceforge.net/projects/genoviz/</url>,":[203],"<url>http://sourceforge.net/projects/useq</url>.":[205]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":13},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":3}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
