{"id":"https://openalex.org/W2136714878","doi":"https://doi.org/10.1186/1471-2105-12-304","title":"Applications of the pipeline environment for visual informatics and genomics computations","display_name":"Applications of the pipeline environment for visual informatics and genomics computations","publication_year":2011,"publication_date":"2011-07-26","ids":{"openalex":"https://openalex.org/W2136714878","doi":"https://doi.org/10.1186/1471-2105-12-304","mag":"2136714878","pmid":"https://pubmed.ncbi.nlm.nih.gov/21791102"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-12-304","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-304","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-304","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/10.1186/1471-2105-12-304","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049834238","display_name":"Ivo D. Dinov","orcid":"https://orcid.org/0000-0003-3825-4375"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ivo D Dinov","raw_affiliation_strings":["Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, CA 90095, USA","Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, 90095, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, CA 90095, USA","institution_ids":["https://openalex.org/I161318765"]},{"raw_affiliation_string":"Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, 90095, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028655046","display_name":"Federica Torri","orcid":null},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]},{"id":"https://openalex.org/I4210156829","display_name":"Research Network (United States)","ror":"https://ror.org/04tgjxk96","country_code":"US","type":"company","lineage":["https://openalex.org/I4210156829"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Federica Torri","raw_affiliation_strings":["Biomedical Informatics Research Network (BIRN), Information Sciences Institute, University of Southern California, Los Angeles, 90292, USA","Departments of Psychiatry and Human Behavior, University of California, Irvine, Irvine, 92617, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Research Network (BIRN), Information Sciences Institute, University of Southern California, Los Angeles, 90292, USA","institution_ids":["https://openalex.org/I4210156829","https://openalex.org/I1174212"]},{"raw_affiliation_string":"Departments of Psychiatry and Human Behavior, University of California, Irvine, Irvine, 92617, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070184927","display_name":"Fab\u00eco Macciardi","orcid":"https://orcid.org/0000-0003-0537-4266"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]},{"id":"https://openalex.org/I4210156829","display_name":"Research Network (United States)","ror":"https://ror.org/04tgjxk96","country_code":"US","type":"company","lineage":["https://openalex.org/I4210156829"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fabio Macciardi","raw_affiliation_strings":["Biomedical Informatics Research Network (BIRN), Information Sciences Institute, University of Southern California, Los Angeles, 90292, USA","Departments of Psychiatry and Human Behavior, University of California, Irvine, Irvine, 92617, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Research Network (BIRN), Information Sciences Institute, University of Southern California, Los Angeles, 90292, USA","institution_ids":["https://openalex.org/I4210156829","https://openalex.org/I1174212"]},{"raw_affiliation_string":"Departments of Psychiatry and Human Behavior, University of California, Irvine, Irvine, 92617, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024805946","display_name":"Petros Petrosyan","orcid":null},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Petros Petrosyan","raw_affiliation_strings":["Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, 90095, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, 90095, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101602083","display_name":"Zhizhong Liu","orcid":"https://orcid.org/0000-0001-6913-0514"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhizhong Liu","raw_affiliation_strings":["Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, 90095, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, 90095, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045208908","display_name":"Alen Zamanyan","orcid":null},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alen Zamanyan","raw_affiliation_strings":["Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, 90095, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, 90095, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029303588","display_name":"Paul Eggert","orcid":"https://orcid.org/0000-0003-2288-8883"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul Eggert","raw_affiliation_strings":["Department of Computer Science, University of California, Los Angeles, Los Angeles, 90095, USA","Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, 90095, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California, Los Angeles, Los Angeles, 90095, USA","institution_ids":["https://openalex.org/I161318765"]},{"raw_affiliation_string":"Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, 90095, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061456225","display_name":"Jonathan Pierce","orcid":null},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan Pierce","raw_affiliation_strings":["Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, 90095, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, 90095, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084352065","display_name":"Alex Genco","orcid":null},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alex Genco","raw_affiliation_strings":["Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, 90095, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, 90095, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101623318","display_name":"James A. Knowles","orcid":"https://orcid.org/0000-0002-3307-5741"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"James A Knowles","raw_affiliation_strings":["Zilkha Neurogenetic Institute, USC Keck School of Medicine, Los Angeles, 90033, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Zilkha Neurogenetic Institute, USC Keck School of Medicine, Los Angeles, 90033, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068522414","display_name":"Andrew P. Clark","orcid":"https://orcid.org/0000-0003-4148-2440"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Andrew P Clark","raw_affiliation_strings":["Zilkha Neurogenetic Institute, USC Keck School of Medicine, Los Angeles, 90033, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Zilkha Neurogenetic Institute, USC Keck School of Medicine, Los Angeles, 90033, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085358934","display_name":"John D. Van Horn","orcid":"https://orcid.org/0000-0003-1537-0816"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John D Van Horn","raw_affiliation_strings":["Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, 90095, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, 90095, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Joseph Ames","orcid":null},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I4210156829","display_name":"Research Network (United States)","ror":"https://ror.org/04tgjxk96","country_code":"US","type":"company","lineage":["https://openalex.org/I4210156829"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph Ames","raw_affiliation_strings":["Biomedical Informatics Research Network (BIRN), Information Sciences Institute, University of Southern California, Los Angeles, 90292, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Research Network (BIRN), Information Sciences Institute, University of Southern California, Los Angeles, 90292, USA","institution_ids":["https://openalex.org/I4210156829","https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085298473","display_name":"Carl Kesselman","orcid":"https://orcid.org/0000-0003-0917-1562"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I4210156829","display_name":"Research Network (United States)","ror":"https://ror.org/04tgjxk96","country_code":"US","type":"company","lineage":["https://openalex.org/I4210156829"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carl Kesselman","raw_affiliation_strings":["Biomedical Informatics Research Network (BIRN), Information Sciences Institute, University of Southern California, Los Angeles, 90292, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Research Network (BIRN), Information Sciences Institute, University of Southern California, Los Angeles, 90292, USA","institution_ids":["https://openalex.org/I4210156829","https://openalex.org/I1174212"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014949118","display_name":"Arthur W. Toga","orcid":"https://orcid.org/0000-0001-7902-3755"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]},{"id":"https://openalex.org/I4210156829","display_name":"Research Network (United States)","ror":"https://ror.org/04tgjxk96","country_code":"US","type":"company","lineage":["https://openalex.org/I4210156829"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arthur W Toga","raw_affiliation_strings":["Biomedical Informatics Research Network (BIRN), Information Sciences Institute, University of Southern California, Los Angeles, 90292, USA","Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, 90095, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Research Network (BIRN), Information Sciences Institute, University of Southern California, Los Angeles, 90292, USA","institution_ids":["https://openalex.org/I4210156829","https://openalex.org/I1174212"]},{"raw_affiliation_string":"Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, 90095, USA","institution_ids":["https://openalex.org/I161318765"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":15,"corresponding_author_ids":["https://openalex.org/A5049834238"],"corresponding_institution_ids":["https://openalex.org/I161318765"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":10.5357,"has_fulltext":true,"cited_by_count":34,"citation_normalized_percentile":{"value":0.97877369,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"12","issue":"1","first_page":"304","last_page":"304"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.6539000272750854,"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":0.6539000272750854,"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":0.17329999804496765,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.030799999833106995,"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":0.7933003902435303},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.7349061965942383},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.646543025970459},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6230552792549133},{"id":"https://openalex.org/keywords/informatics","display_name":"Informatics","score":0.6182550191879272},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.49518147110939026},{"id":"https://openalex.org/keywords/health-informatics-tools","display_name":"Health informatics tools","score":0.47244885563850403},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.4329957365989685},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.42152276635169983},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3610457181930542},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.28078293800354004},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.18837660551071167},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.15678992867469788}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7933003902435303},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.7349061965942383},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.646543025970459},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6230552792549133},{"id":"https://openalex.org/C191630685","wikidata":"https://www.wikidata.org/wiki/Q4027615","display_name":"Informatics","level":2,"score":0.6182550191879272},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.49518147110939026},{"id":"https://openalex.org/C167785021","wikidata":"https://www.wikidata.org/wiki/Q5691083","display_name":"Health informatics tools","level":3,"score":0.47244885563850403},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4329957365989685},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.42152276635169983},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3610457181930542},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.28078293800354004},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.18837660551071167},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.15678992867469788},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008491","descriptor_name":"Medical Informatics Applications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008491","descriptor_name":"Medical Informatics Applications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008491","descriptor_name":"Medical Informatics Applications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008491","descriptor_name":"Medical Informatics Applications","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D048088","descriptor_name":"Informatics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D048088","descriptor_name":"Informatics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D048088","descriptor_name":"Informatics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D048088","descriptor_name":"Informatics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1186/1471-2105-12-304","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-304","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-304","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:21791102","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21791102","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:air.unimi.it:2434/266527","is_oa":true,"landing_page_url":"http://hdl.handle.net/2434/266527","pdf_url":"http://hdl.handle.net/2434/266527","source":{"id":"https://openalex.org/S4306400516","display_name":"Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I189158943","host_organization_name":"University of Milan","host_organization_lineage":["https://openalex.org/I189158943"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:0f6f196721744e5aab4796e80c54ea36","is_oa":true,"landing_page_url":"https://doaj.org/article/0f6f196721744e5aab4796e80c54ea36","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 12, Iss 1, p 304 (2011)","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt5cn2s39h","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/5cn2s39h","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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, vol 12, iss 1","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt7rg152gp","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/7rg152gp","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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 12, iss 1","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2201312","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3199760","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:qt7rg152gp","is_oa":false,"landing_page_url":"http://www.escholarship.org/uc/item/7rg152gp","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Dinov, Ivo D; Torri, Federica; Macciardi, Fabio; Petrosyan, Petros; Liu, Zhizhong; Zamanyan, Alen; \u00c2\u00a0et al.(2011). Applications of the Pipeline Environment for Visual Informatics and Genomics Computations. BMC Bioinformatics, 12(1), 304. doi: http://dx.doi.org/10.1186/1471-2105-12-304. Retrieved from: http://www.escholarship.org/uc/item/7rg152gp","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-12-304","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-304","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-304","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":[{"score":0.6299999952316284,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G2101374638","display_name":null,"funder_award_id":"U24-RR021992","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G316304657","display_name":null,"funder_award_id":"U24-RR025736","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3630907223","display_name":null,"funder_award_id":"P41 RR013642","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6241014215","display_name":null,"funder_award_id":"U54 RR021813","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320308571","display_name":"North Carolina Biotechnology Center","ror":"https://ror.org/03hj4jr80"},{"id":"https://openalex.org/F4320308668","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60"},{"id":"https://openalex.org/F4320316438","display_name":"Georgia Clinical and Translational Science Alliance","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2136714878.pdf","grobid_xml":"https://content.openalex.org/works/W2136714878.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W71547456","https://openalex.org/W151680184","https://openalex.org/W323641075","https://openalex.org/W1505387628","https://openalex.org/W1529006120","https://openalex.org/W1577070011","https://openalex.org/W1583268303","https://openalex.org/W1651609297","https://openalex.org/W1828735316","https://openalex.org/W1835740130","https://openalex.org/W1970716201","https://openalex.org/W1971098996","https://openalex.org/W1974046375","https://openalex.org/W1982405319","https://openalex.org/W1983833794","https://openalex.org/W1990073900","https://openalex.org/W1993785488","https://openalex.org/W2014683913","https://openalex.org/W2022696062","https://openalex.org/W2039605938","https://openalex.org/W2043423323","https://openalex.org/W2050274079","https://openalex.org/W2058651674","https://openalex.org/W2075193814","https://openalex.org/W2079062663","https://openalex.org/W2108234281","https://openalex.org/W2112113834","https://openalex.org/W2112846847","https://openalex.org/W2115321097","https://openalex.org/W2124985265","https://openalex.org/W2126043693","https://openalex.org/W2135839296","https://openalex.org/W2136482257","https://openalex.org/W2139747296","https://openalex.org/W2142776558","https://openalex.org/W2144255051","https://openalex.org/W2148300596","https://openalex.org/W2149791927","https://openalex.org/W2150265050","https://openalex.org/W2150321679","https://openalex.org/W2151327690","https://openalex.org/W2167164378","https://openalex.org/W2168103533","https://openalex.org/W2485674704","https://openalex.org/W2540625579","https://openalex.org/W3047671819","https://openalex.org/W4233882242"],"related_works":["https://openalex.org/W2463183163","https://openalex.org/W2017123803","https://openalex.org/W2320705913","https://openalex.org/W2974071312","https://openalex.org/W2005011662","https://openalex.org/W2955949264","https://openalex.org/W4311292698","https://openalex.org/W4309236105","https://openalex.org/W3174814859","https://openalex.org/W2979004191"],"abstract_inverted_index":{"BACKGROUND:":[0],"Contemporary":[1],"informatics":[2,73,86,98,127,145,221,237,251],"and":[3,9,28,31,51,82,100,111,123,160,166,199,219,231,254,272,279,293,296,301],"genomics":[4,80],"research":[5],"require":[6],"efficient,":[7],"flexible":[8,212],"robust":[10],"management":[11,77],"of":[12,25,53,65,78,85,95,113,125,139,175,184,195,233,236,250,281,289,303],"large":[13],"heterogeneous":[14],"data,":[15],"advanced":[16,54,263],"computational":[17,26,40,244,282],"tools,":[18,81,291],"powerful":[19],"visualization,":[20],"reliable":[21],"hardware":[22,106],"infrastructure,":[23],"interoperability":[24,84,232],"resources,":[27],"detailed":[29],"data":[30,55,164],"analysis-protocol":[32],"provenance.":[33],"The":[34,205,223,239,275],"Pipeline":[35,68,120,131,177,207,225,240],"is":[36],"a":[37,189,211,247],"client-server":[38,241],"distributed":[39,220],"environment":[41,69,180,208],"that":[42],"facilitates":[43,286],"the":[44,63,66,83,92,108,119,130,173,176,196,200,229,287,298,307],"visual":[45,115],"graphical":[46,76,121,178,213],"construction,":[47],"execution,":[48],"monitoring,":[49],"validation":[50,110,278,300],"dissemination":[52,280],"analysis":[56,116],"protocols.":[57],"RESULTS:":[58],"This":[59],"paper":[60],"reports":[61],"on":[62],"applications":[64],"LONI":[67,206],"to":[70,104,181,246,262],"address":[71],"two":[72],"challenges":[74],"-":[75],"diverse":[79,126,234],"software.":[87],"Specifically,":[88],"this":[89],"manuscript":[90],"presents":[91],"concrete":[93],"details":[94],"deploying":[96],"general":[97],"suites":[99],"individual":[101],"software":[102],"tools":[103,128],"new":[105,114],"infrastructures,":[107],"design,":[109],"execution":[112,202],"protocols":[117,292],"via":[118,129],"interface,":[122],"integration":[124,183],"eXtensible":[132],"Markup":[133],"Language":[134],"syntax.":[135],"We":[136],"demonstrate":[137,172],"each":[138],"these":[140],"processes":[141],"using":[142],"several":[143],"established":[144],"packages":[146],"(e.g.,":[147,265],"miBLAST,":[148],"EMBOSS,":[149],"mrFAST,":[150],"GWASS,":[151],"MAQ,":[152],"SAMtools,":[153],"Bowtie)":[154],"for":[155,192,215],"basic":[156,271],"local":[157],"sequence":[158],"alignment":[159],"search,":[161],"molecular":[162],"biology":[163],"analysis,":[165],"genome-wide":[167],"association":[168],"studies.":[169],"These":[170],"examples":[171],"power":[174,245],"workflow":[179],"enable":[182],"bioinformatics":[185],"resources":[186],"which":[187],"provide":[188],"well-defined":[190],"syntax":[191],"dynamic":[193],"specification":[194],"input/output":[197],"parameters":[198],"run-time":[201],"controls.":[203],"CONCLUSIONS:":[204],"http://pipeline.loni.ucla.edu":[209],"provides":[210,243],"infrastructure":[214],"efficient":[216],"biomedical":[217],"computing":[218],"research.":[222],"interactive":[224],"resource":[226],"manager":[227],"enables":[228,297],"utilization":[230],"types":[235],"resources.":[238],"model":[242],"broad":[248],"spectrum":[249],"investigators--experienced":[252],"developers":[253],"novice":[255],"users,":[256],"user":[257],"with":[258],"or":[259],"without":[260],"access":[261],"computational-resources":[264],"Grid,":[266],"data),":[267],"as":[268,270],"well":[269],"translational":[273],"scientists.":[274],"open":[276],"development,":[277],"networks":[283],"(pipeline":[284],"workflows)":[285],"sharing":[288],"knowledge,":[290],"best":[294],"practices,":[295],"unbiased":[299],"replication":[302],"scientific":[304],"findings":[305],"by":[306],"entire":[308],"community.":[309]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":3}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
