{"id":"https://openalex.org/W3044149854","doi":"https://doi.org/10.1145/3311790.3396634","title":"Building an Interactive Workbench Environment for Single Cell Genomics Applications","display_name":"Building an Interactive Workbench Environment for Single Cell Genomics Applications","publication_year":2020,"publication_date":"2020-07-22","ids":{"openalex":"https://openalex.org/W3044149854","doi":"https://doi.org/10.1145/3311790.3396634","mag":"3044149854"},"language":"en","primary_location":{"id":"doi:10.1145/3311790.3396634","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3311790.3396634","pdf_url":null,"source":{"id":"https://openalex.org/S4306523034","display_name":"Practice and Experience in Advanced Research Computing","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Practice and Experience in Advanced Research Computing","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5111323964","display_name":"D. Balamurugan","orcid":null},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"D Balamurugan","raw_affiliation_strings":["Rutgers University, USA"],"affiliations":[{"raw_affiliation_string":"Rutgers University, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047834758","display_name":"Kristina Plazonic","orcid":null},"institutions":[{"id":"https://openalex.org/I3131869939","display_name":"NBCUniversal (United States)","ror":"https://ror.org/05kgq6h80","country_code":"US","type":"company","lineage":["https://openalex.org/I3131869939"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kristina Plazonic","raw_affiliation_strings":["NBC Universal, USA"],"affiliations":[{"raw_affiliation_string":"NBC Universal, USA","institution_ids":["https://openalex.org/I3131869939"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022126773","display_name":"Kevin Abbey","orcid":null},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kevin Abbey","raw_affiliation_strings":["Rutgers University, USA"],"affiliations":[{"raw_affiliation_string":"Rutgers University, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102259631","display_name":"Seema Husain","orcid":null},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Seema Husain","raw_affiliation_strings":["Rutgers University, USA"],"affiliations":[{"raw_affiliation_string":"Rutgers University, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071341014","display_name":"Neeraja Syed","orcid":null},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Neeraja Syed","raw_affiliation_strings":["Rutgers University, USA"],"affiliations":[{"raw_affiliation_string":"Rutgers University, USA","institution_ids":["https://openalex.org/I102322142"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5111323964"],"corresponding_institution_ids":["https://openalex.org/I102322142"],"apc_list":null,"apc_paid":null,"fwci":0.0829,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.43920724,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"125","last_page":"131"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998000264167786,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998000264167786,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9767000079154968,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9757000207901001,"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/workbench","display_name":"Workbench","score":0.9439918994903564},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.8386850357055664},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.755293607711792},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6943787336349487},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4341089129447937},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3739508390426636},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.3402622938156128},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.27483445405960083},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.22631573677062988},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2203768491744995},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.12171736359596252},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.09647423028945923}],"concepts":[{"id":"https://openalex.org/C2779145975","wikidata":"https://www.wikidata.org/wiki/Q347690","display_name":"Workbench","level":3,"score":0.9439918994903564},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8386850357055664},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.755293607711792},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6943787336349487},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4341089129447937},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3739508390426636},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.3402622938156128},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.27483445405960083},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.22631573677062988},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2203768491744995},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.12171736359596252},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.09647423028945923},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3311790.3396634","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3311790.3396634","pdf_url":null,"source":{"id":"https://openalex.org/S4306523034","display_name":"Practice and Experience in Advanced Research Computing","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Practice and Experience in Advanced Research Computing","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6100000143051147,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1899011294","https://openalex.org/W1975623012","https://openalex.org/W1984883254","https://openalex.org/W2013434113","https://openalex.org/W2078962046","https://openalex.org/W2087242711","https://openalex.org/W2099744871","https://openalex.org/W2110417468","https://openalex.org/W2111607395","https://openalex.org/W2115570304","https://openalex.org/W2308670510","https://openalex.org/W2605897695","https://openalex.org/W2612519453","https://openalex.org/W2784067590","https://openalex.org/W2794480084","https://openalex.org/W2800392236","https://openalex.org/W2804145951","https://openalex.org/W2809616137","https://openalex.org/W2885307522","https://openalex.org/W2917207851","https://openalex.org/W2940602161","https://openalex.org/W2943761765","https://openalex.org/W2951506174","https://openalex.org/W4213108508","https://openalex.org/W6947937829"],"related_works":["https://openalex.org/W2388509490","https://openalex.org/W2109648960","https://openalex.org/W2166015079","https://openalex.org/W2050384624","https://openalex.org/W2776888796","https://openalex.org/W2388480422","https://openalex.org/W2624268110","https://openalex.org/W2951120646","https://openalex.org/W2356913294","https://openalex.org/W2903672016"],"abstract_inverted_index":{"We":[0],"discuss":[1],"the":[2,16,37,40,44,58,61,84,89,97],"procedure":[3],"to":[4],"build":[5],"an":[6,25],"interactive":[7],"workbench":[8],"environment":[9],"for":[10,103],"single":[11,30],"cell":[12,31],"genomics":[13],"applications":[14],"with":[15],"Open":[17],"OnDemand":[18],"(OOD)":[19],"science":[20],"gateway.":[21],"In":[22],"our":[23],"approach,":[24],"end-user":[26],"submits":[27],"a":[28,54,68],"complex":[29],"RNA":[32],"sequencing":[33],"(scRNA)":[34],"pipeline,":[35],"checks":[36],"status":[38],"of":[39,48,81],"job,":[41],"and":[42,66],"visualizes":[43],"output":[45],"results.":[46],"All":[47],"these":[49],"tasks":[50],"are":[51],"accomplished":[52],"through":[53],"web":[55],"browser,":[56],"relieving":[57],"users":[59],"from":[60],"complexities":[62],"involved":[63],"in":[64,75,83],"developing":[65],"handling":[67],"large-scale":[69],"workflow.":[70,105],"Our":[71],"approach":[72,99],"helped":[73],"researchers":[74],"processing":[76],"several":[77],"input":[78],"data":[79],"sets":[80],"scRNA":[82,95],"campus":[85],"HPC":[86],"cluster.":[87],"Although":[88],"current":[90],"work":[91],"is":[92],"focused":[93],"on":[94],"analysis,":[96],"same":[98],"can":[100],"be":[101],"extended":[102],"any":[104]},"counts_by_year":[{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
