{"id":"https://openalex.org/W2880001313","doi":"https://doi.org/10.1145/3219104.3219141","title":"Building a Science Gateway For Processing and Modeling Sequencing Data Via Apache Airavata","display_name":"Building a Science Gateway For Processing and Modeling Sequencing Data Via Apache Airavata","publication_year":2018,"publication_date":"2018-07-12","ids":{"openalex":"https://openalex.org/W2880001313","doi":"https://doi.org/10.1145/3219104.3219141","mag":"2880001313","pmid":"https://pubmed.ncbi.nlm.nih.gov/31598610","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/6785190"},"language":"en","primary_location":{"id":"doi:10.1145/3219104.3219141","doi":"https://doi.org/10.1145/3219104.3219141","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3219104.3219141","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,"listed_in":["cwts-core"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Practice and Experience on Advanced Research Computing","raw_type":"proceedings-article"},"volume":null,"type":"conference-paper","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6785190","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100781872","display_name":"Zhong Wang","orcid":"https://orcid.org/0000-0002-6307-0458","observed_orcids":["https://orcid.org/0000-0002-6307-0458"]},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I4210151139","display_name":"New York State College of Veterinary Medicine","ror":"https://ror.org/04r17kf39","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4210151139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhong Wang","raw_affiliation_strings":["Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I4210151139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027985692","display_name":"Marcus Aaron Christie","orcid":"https://orcid.org/0000-0001-5458-9947","observed_orcids":["https://orcid.org/0000-0001-5458-9947"]},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]},{"id":"https://openalex.org/I592451","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98","country_code":"US","type":"education","lineage":["https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marcus A. Christie","raw_affiliation_strings":["Science Gateways Research Center, Pervasive Technology Institute, Indiana University, Bloomington, IN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Science Gateways Research Center, Pervasive Technology Institute, Indiana University, Bloomington, IN","institution_ids":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075415797","display_name":"Eroma Abeysinghe","orcid":"https://orcid.org/0000-0002-1801-2515","observed_orcids":["https://orcid.org/0000-0002-1801-2515"]},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]},{"id":"https://openalex.org/I592451","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98","country_code":"US","type":"education","lineage":["https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eroma Abeysinghe","raw_affiliation_strings":["Science Gateways Research Center, Pervasive Technology Institute, Indiana University, Bloomington, IN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Science Gateways Research Center, Pervasive Technology Institute, Indiana University, Bloomington, IN","institution_ids":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080074043","display_name":"Tinyi Chu","orcid":"https://orcid.org/0000-0003-3369-6692","observed_orcids":["https://orcid.org/0000-0003-3369-6692"]},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tinyi Chu","raw_affiliation_strings":["Cornell University, Ithaca, NY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cornell University, Ithaca, NY","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037778136","display_name":"Suresh Marru","orcid":"https://orcid.org/0000-0002-6374-095X","observed_orcids":["https://orcid.org/0000-0002-6374-095X"]},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]},{"id":"https://openalex.org/I592451","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98","country_code":"US","type":"education","lineage":["https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Suresh Marru","raw_affiliation_strings":["Science Gateways Research Center, Pervasive Technology Institute, Indiana University, Bloomington, IN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Science Gateways Research Center, Pervasive Technology Institute, Indiana University, Bloomington, IN","institution_ids":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082786549","display_name":"Marlon Pierce","orcid":"https://orcid.org/0000-0002-9582-5712","observed_orcids":["https://orcid.org/0000-0002-9582-5712"]},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]},{"id":"https://openalex.org/I592451","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98","country_code":"US","type":"education","lineage":["https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marlon Pierce","raw_affiliation_strings":["Science Gateways Research Center, Pervasive Technology Institute, Indiana University, Bloomington, IN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Science Gateways Research Center, Pervasive Technology Institute, Indiana University, Bloomington, IN","institution_ids":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024923108","display_name":"Charles G. Danko","orcid":"https://orcid.org/0000-0002-1999-7125","observed_orcids":["https://orcid.org/0000-0002-1999-7125"]},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I4210151139","display_name":"New York State College of Veterinary Medicine","ror":"https://ror.org/04r17kf39","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4210151139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Charles G. Danko","raw_affiliation_strings":["Baker Institute for Animal Health and Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Baker Institute for Animal Health and Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I4210151139"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.8116,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.85245297,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"2018","issue":null,"first_page":"1","last_page":"7"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.6894999742507935,"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":0.6894999742507935,"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/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.16760000586509705,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.10379999876022339,"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/science-gateways","display_name":"science gateways","score":0.9649999737739563},{"id":"https://openalex.org/keywords/xsede","display_name":"XSEDE","score":0.7490000128746033},{"id":"https://openalex.org/keywords/high-performance-computing","display_name":"high-performance computing","score":0.8199999928474426},{"id":"https://openalex.org/keywords/nascent-rna-sequencing","display_name":"nascent RNA sequencing","score":0.9539999961853027},{"id":"https://openalex.org/keywords/mammalian-genomes","display_name":"mammalian genomes","score":0.968999981880188},{"id":"https://openalex.org/keywords/gpu-computing","display_name":"GPU computing","score":0.9729999899864197}],"concepts":[{"id":"https://openalex.org/C2777710495","wikidata":"https://www.wikidata.org/wiki/Q5527195","display_name":"Gateway (web page)","level":2,"score":0.8128896951675415},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8058962821960449},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.6058070063591003},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.4719492495059967},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.459267258644104},{"id":"https://openalex.org/C187713609","wikidata":"https://www.wikidata.org/wiki/Q2465461","display_name":"Default gateway","level":2,"score":0.45032256841659546},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.36361533403396606},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3074512183666229},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.18831291794776917}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1145/3219104.3219141","doi":"https://doi.org/10.1145/3219104.3219141","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3219104.3219141","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,"listed_in":["cwts-core"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Practice and Experience on Advanced Research Computing","raw_type":"proceedings-article"},{"id":"pmid:31598610","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31598610","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,"listed_in":[],"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":"Practice and Experience in Advanced Research Computing 2018 : Seamless Creativity : July 22-26 2017, Pittsburgh, Pennsylvania. Practice and Experience in Advanced Research Computing (Conference) (2018 : Pittsburgh, Pa.)","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:5744690","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6785190","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,"listed_in":[],"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":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6785190","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6785190","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Pract Exp Adv Res Comput 2018 (2018)","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:europepmc.org:5744690","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6785190","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,"listed_in":[],"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":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.4943999946117401}],"study_designs":[],"awards":[{"id":"https://openalex.org/G1173569537","display_name":"Mapping RNA polymerase in tissue samples with ChRO-seq.","funder_award_id":"5r01hg009309-05","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G984684530","display_name":null,"funder_award_id":"R01-HG009309","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1501531009","https://openalex.org/W1505191356","https://openalex.org/W1985567287","https://openalex.org/W1997590968","https://openalex.org/W2007844697","https://openalex.org/W2028302194","https://openalex.org/W2040890279","https://openalex.org/W2043701535","https://openalex.org/W2069294792","https://openalex.org/W2070679139","https://openalex.org/W2087724241","https://openalex.org/W2120500419","https://openalex.org/W2128016314","https://openalex.org/W2129154270","https://openalex.org/W2139427967","https://openalex.org/W2146728635","https://openalex.org/W2149109760","https://openalex.org/W2172627993","https://openalex.org/W2264017649","https://openalex.org/W2323326409","https://openalex.org/W2346143774","https://openalex.org/W2479945688","https://openalex.org/W2496186988","https://openalex.org/W2497005299","https://openalex.org/W2522987496","https://openalex.org/W2592811885","https://openalex.org/W2597980747","https://openalex.org/W2632341321","https://openalex.org/W2731648980","https://openalex.org/W2731998311","https://openalex.org/W2741781568","https://openalex.org/W2750772406","https://openalex.org/W2765285264","https://openalex.org/W2950354537","https://openalex.org/W2963457143"],"related_works":["https://openalex.org/W6958838288","https://openalex.org/W2415084227","https://openalex.org/W6912710668","https://openalex.org/W6931554247","https://openalex.org/W2857907774","https://openalex.org/W2536682495","https://openalex.org/W2069037310","https://openalex.org/W4403868483","https://openalex.org/W4414903363","https://openalex.org/W3005595194"],"abstract_inverted_index":{"The":[0,187,220],"amount":[1],"of":[2,25,45,135,207],"DNA":[3],"sequencing":[4,18,26,185],"data":[5,27],"has":[6],"been":[7],"exponentially":[8],"growing":[9],"during":[10],"the":[11,82,92,113,136,146,168,205],"past":[12],"decade":[13],"due":[14],"to":[15,54,94,153,163],"advances":[16],"in":[17,43,179],"technology.":[19],"Processing":[20],"and":[21,48,72,87,139,156,196,213],"modeling":[22],"large":[23],"amounts":[24],"can":[28,49],"be":[29,50],"computationally":[30],"intractable":[31],"for":[32,60,108,116,148,167,175,218],"desktop":[33],"computing":[34,38,46,106,131,173,199],"platforms.":[35],"High":[36],"performance":[37],"(HPC)":[39],"resources":[40,93,125,147],"offer":[41],"advantages":[42],"terms":[44],"power,":[47],"a":[51,104,165,193],"general":[52],"solution":[53],"these":[55],"problems.":[56],"Using":[57],"HPCs":[58,71],"directly":[59],"computational":[61],"needs":[62],"requires":[63],"skilled":[64],"users":[65,86,90,192],"who":[66],"know":[67],"their":[68],"way":[69],"around":[70],"acquiring":[73],"such":[74],"skills":[75],"take":[76],"time.":[77],"Science":[78,138],"gateways":[79],"acts":[80],"as":[81],"middle":[83],"layer":[84],"between":[85],"HPCs,":[88],"providing":[89],"with":[91],"accomplish":[95],"compute-intensive":[96],"tasks":[97],"without":[98],"requiring":[99],"specialized":[100,208],"expertise.":[101],"We":[102,159],"developed":[103],"web-based":[105],"platform":[107,132,162],"genome":[109],"biologists":[110],"by":[111],"customizing":[112],"PHP":[114],"Gateway":[115],"Airavata":[117],"(PGA)":[118],"framework":[119],"that":[120],"accesses":[121],"publicly":[122],"accessible":[123],"HPC":[124,217],"via":[126],"Apache":[127],"Airavata.":[128],"This":[129],"web":[130],"takes":[133],"advantage":[134],"Extreme":[137],"Engineering":[140],"Discovery":[141],"Environment":[142],"(XSEDE)":[143],"which":[144],"provides":[145,190],"gateway":[149,166,189,222],"development,":[150],"including":[151],"access":[152],"CPU,":[154],"GPU,":[155],"storage":[157],"resources.":[158],"used":[160],"this":[161],"develop":[164],"dREG":[169,188,221],"algorithm,":[170],"an":[171,216],"online":[172],"tool":[174],"finding":[176],"functional":[177],"regions":[178],"mammalian":[180],"genomes":[181],"using":[182],"nascent":[183],"RNA":[184],"data.":[186],"its":[191],"free,":[194],"powerful":[195],"user-friendly":[197],"GPU":[198],"resource":[200],"based":[201],"on":[202,215],"XSEDE,":[203],"circumventing":[204],"need":[206],"knowledge":[209],"about":[210],"installation,":[211],"configuration,":[212],"execution":[214],"biologists.":[219],"is":[223],"available":[224],"at:":[225],"https://dREG.dnasequence.org/.":[226]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":1}],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2018-07-19T00:00:00"}