{"id":"https://openalex.org/W2136834914","doi":"https://doi.org/10.1093/bioinformatics/bts122","title":"SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer","display_name":"SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer","publication_year":2012,"publication_date":"2012-03-13","ids":{"openalex":"https://openalex.org/W2136834914","doi":"https://doi.org/10.1093/bioinformatics/bts122","mag":"2136834914","pmid":"https://pubmed.ncbi.nlm.nih.gov/22419785"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts122","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts122","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/9/1276/48874983/bioinformatics_28_9_1276.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/9/1276/48874983/bioinformatics_28_9_1276.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001072827","display_name":"Kris Popendorf","orcid":null},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kris Popendorf","raw_affiliation_strings":["Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan","institution_ids":["https://openalex.org/I203951103"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025573915","display_name":"Yasubumi Sakakibara","orcid":"https://orcid.org/0000-0002-6932-3452"},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yasubumi Sakakibara","raw_affiliation_strings":["Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan","institution_ids":["https://openalex.org/I203951103"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5025573915"],"corresponding_institution_ids":["https://openalex.org/I203951103"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.5297,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.6597006,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"28","issue":"9","first_page":"1276","last_page":"1277"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.3077000081539154,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.3077000081539154,"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":0.08879999816417694,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.04259999841451645,"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":0.7944153547286987},{"id":"https://openalex.org/keywords/opengl","display_name":"OpenGL","score":0.7298004627227783},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.7227678298950195},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5423266887664795},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.5294803380966187},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5291925668716431},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.522517204284668},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.48401471972465515},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.4775996208190918},{"id":"https://openalex.org/keywords/mac-os","display_name":"Mac OS","score":0.43294304609298706},{"id":"https://openalex.org/keywords/os-x","display_name":"OS X","score":0.4222601056098938},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.346283495426178},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.1967240273952484}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7944153547286987},{"id":"https://openalex.org/C2778305236","wikidata":"https://www.wikidata.org/wiki/Q178570","display_name":"OpenGL","level":3,"score":0.7298004627227783},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7227678298950195},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5423266887664795},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.5294803380966187},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5291925668716431},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.522517204284668},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.48401471972465515},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.4775996208190918},{"id":"https://openalex.org/C522133331","wikidata":"https://www.wikidata.org/wiki/Q43627","display_name":"Mac OS","level":3,"score":0.43294304609298706},{"id":"https://openalex.org/C515153823","wikidata":"https://www.wikidata.org/wiki/Q14116","display_name":"OS X","level":3,"score":0.4222601056098938},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.346283495426178},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.1967240273952484},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bts122","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts122","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/9/1276/48874983/bioinformatics_28_9_1276.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22419785","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22419785","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts122","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts122","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/9/1276/48874983/bioinformatics_28_9_1276.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.4000000059604645}],"awards":[{"id":"https://openalex.org/G1657907276","display_name":"Comprehensive analysis of functional non-coding RNAs in cancer genome on multistage carcinogenesis","funder_award_id":"23241066","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G8124787675","display_name":"Platform of large scale and high quality genomics and bioinformatics: Towards the advancement of genome sciences in academia","funder_award_id":"221S0002","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1968475238","https://openalex.org/W2019196984","https://openalex.org/W2021341670","https://openalex.org/W2108234281","https://openalex.org/W2112113834","https://openalex.org/W2122270655","https://openalex.org/W2124985265","https://openalex.org/W2129785061","https://openalex.org/W2140154634","https://openalex.org/W2152710395","https://openalex.org/W2295329974","https://openalex.org/W4244659560"],"related_works":["https://openalex.org/W2373739385","https://openalex.org/W2348591816","https://openalex.org/W2999985154","https://openalex.org/W2353068760","https://openalex.org/W2358677151","https://openalex.org/W2354911658","https://openalex.org/W2361033084","https://openalex.org/W3098339315","https://openalex.org/W2114099042","https://openalex.org/W2161971256"],"abstract_inverted_index":{"SUMMARY:":[0],"Existing":[1],"SAM":[2],"visualization":[3,77],"tools":[4,22],"like":[5,23],"'samtools":[6],"tview'":[7],"(Li":[8],"et":[9,26],"al.,":[10,27],"2009)":[11],"are":[12,29,127],"limited":[13,30],"to":[14,31,47],"a":[15,32,75],"small":[16,34],"region":[17],"of":[18,36,91,98,104],"the":[19],"genome,":[20],"and":[21,38,51,87,95,125],"Tablet":[24],"(Milne":[25],"2010)":[28],"relatively":[33],"number":[35],"reads":[37],"may":[39],"fail":[40],"outright":[41],"on":[42],"large":[43],"datasets.":[44],"We":[45,69],"need":[46],"visualize":[48],"complex":[49,99],"ChIP-Seq":[50],"RNA-Seq":[52],"features":[53],"such":[54,66],"as":[55,57,59,67],"polarity":[56],"well":[58],"coverage":[60],"across":[61,106],"whole":[62],"3":[63],"Gbp":[64],"genomes":[65],"Human.":[68],"have":[70],"addressed":[71],"these":[72],"problems":[73],"in":[74,116],"lightweight":[76],"system":[78],"called":[79],"SAMSCOPE":[80,92,113],"accelerated":[81],"by":[82],"OpenGL.":[83],"The":[84,112],"extensive":[85],"pre-processing":[86],"fast":[88],"OpenGL":[89],"interface":[90],"provides":[93],"instantaneous":[94],"intuitive":[96],"browsing":[97],"data":[100],"at":[101],"all":[102],"levels":[103],"detail":[105],"multiple":[107],"experiments.":[108],"AVAILABILITY":[109],"AND":[110],"IMPLEMENTATION:":[111],"software,":[114],"implemented":[115],"C++":[117],"for":[118],"Linux,":[119],"with":[120],"source":[121],"code,":[122],"binary":[123],"packages":[124],"documentation":[126],"freely":[128],"available":[129],"from":[130],"http://samscope.dna.bio.keio.ac.jp.":[131]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}
