{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,6,18]],"date-time":"2025-06-18T04:33:51Z","timestamp":1750221231857,"version":"3.41.0"},"publisher-location":"New York, NY, USA","reference-count":40,"publisher":"ACM","license":[{"start":{"date-parts":[[2018,7,22]],"date-time":"2018-07-22T00:00:00Z","timestamp":1532217600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.acm.org\/publications\/policies\/copyright_policy#Background"}],"funder":[{"name":"NHGRI","award":["R01-HG009309"],"award-info":[{"award-number":["R01-HG009309"]}]},{"name":"XSEDE allocations","award":["TG-BIO160048 and TG-MCB160061"],"award-info":[{"award-number":["TG-BIO160048 and TG-MCB160061"]}]},{"name":"NSF award","award":["1547611"],"award-info":[{"award-number":["1547611"]}]}],"content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2018,7,22]]},"DOI":"10.1145\/3219104.3219141","type":"proceedings-article","created":{"date-parts":[[2018,7,12]],"date-time":"2018-07-12T17:46:44Z","timestamp":1531417604000},"page":"1-7","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["Building a Science Gateway For Processing and Modeling Sequencing Data Via Apache Airavata"],"prefix":"10.1145","author":[{"given":"Zhong","family":"Wang","sequence":"first","affiliation":[{"name":"Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marcus A.","family":"Christie","sequence":"additional","affiliation":[{"name":"Science Gateways Research Center, Pervasive Technology Institute, Indiana University, Bloomington, IN"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eroma","family":"Abeysinghe","sequence":"additional","affiliation":[{"name":"Science Gateways Research Center, Pervasive Technology Institute, Indiana University, Bloomington, IN"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tinyi","family":"Chu","sequence":"additional","affiliation":[{"name":"Cornell University, Ithaca, NY"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Suresh","family":"Marru","sequence":"additional","affiliation":[{"name":"Science Gateways Research Center, Pervasive Technology Institute, Indiana University, Bloomington, IN"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marlon","family":"Pierce","sequence":"additional","affiliation":[{"name":"Science Gateways Research Center, Pervasive Technology Institute, Indiana University, Bloomington, IN"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Charles G.","family":"Danko","sequence":"additional","affiliation":[{"name":"Baker Institute for Animal Health and Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"320","published-online":{"date-parts":[[2018,7,22]]},"reference":[{"key":"e_1_3_2_1_1_1","unstructured":"2018. Genome Cloud Computing - Amazon Web Service (AWS). (2018). https:\/\/aws.amazon.com\/en\/health\/genomics\/  2018. Genome Cloud Computing - Amazon Web Service (AWS). (2018). https:\/\/aws.amazon.com\/en\/health\/genomics\/"},{"key":"e_1_3_2_1_2_1","unstructured":"2018. SciGaP gateway. (2018). https:\/\/scigap.org\/  2018. SciGaP gateway. (2018). https:\/\/scigap.org\/"},{"key":"e_1_3_2_1_3_1","unstructured":"2018. Tus - resumable file uploads. (2018). https:\/\/tus.io\/  2018. Tus - resumable file uploads. (2018). https:\/\/tus.io\/"},{"key":"e_1_3_2_1_4_1","volume-title":"Daniel Blankenberg, Dave Bouvier, Martin \u010cech, John Chilton, Dave Clements, Nate Coraor, Carl Eberhard, et al.","author":"Afgan Enis","year":"2016","unstructured":"Enis Afgan , Dannon Baker , Marius Van den Beek , Daniel Blankenberg, Dave Bouvier, Martin \u010cech, John Chilton, Dave Clements, Nate Coraor, Carl Eberhard, et al. 2016 . The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic acids research 44, W1 (2016), W3--W10. Enis Afgan, Dannon Baker, Marius Van den Beek, Daniel Blankenberg, Dave Bouvier, Martin \u010cech, John Chilton, Dave Clements, Nate Coraor, Carl Eberhard, et al. 2016. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic acids research 44, W1 (2016), W3--W10."},{"key":"e_1_3_2_1_5_1","volume-title":"Predicting the sequence specificities of DNA-and RNA-binding proteins by deep learning. Nature biotechnology 33, 8","author":"Alipanahi Babak","year":"2015","unstructured":"Babak Alipanahi , Andrew Delong , Matthew T Weirauch , and Brendan J Frey . 2015. Predicting the sequence specificities of DNA-and RNA-binding proteins by deep learning. Nature biotechnology 33, 8 ( 2015 ), 831. Babak Alipanahi, Andrew Delong, Matthew T Weirauch, and Brendan J Frey. 2015. Predicting the sequence specificities of DNA-and RNA-binding proteins by deep learning. Nature biotechnology 33, 8 (2015), 831."},{"key":"e_1_3_2_1_6_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0141287"},{"key":"e_1_3_2_1_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw599"},{"key":"e_1_3_2_1_8_1","volume-title":"Near-optimal probabilistic RNA-seq quantification. Nature biotechnology 34, 5","author":"Bray Nicolas L","year":"2016","unstructured":"Nicolas L Bray , Harold Pimentel , P\u00e1ll Melsted , and Lior Pachter . 2016. Near-optimal probabilistic RNA-seq quantification. Nature biotechnology 34, 5 ( 2016 ), 525. Nicolas L Bray, Harold Pimentel, P\u00e1ll Melsted, and Lior Pachter. 2016. Near-optimal probabilistic RNA-seq quantification. Nature biotechnology 34, 5 (2016), 525."},{"key":"e_1_3_2_1_9_1","volume-title":"Are next-generation sequencing tools ready for the cloud? Trends in biotechnology 35, 6","author":"Celesti Antonio","year":"2017","unstructured":"Antonio Celesti , Fabrizio Celesti , Maria Fazio , Placido Bramanti , and Massimo Villari . 2017. Are next-generation sequencing tools ready for the cloud? Trends in biotechnology 35, 6 ( 2017 ), 486--489. Antonio Celesti, Fabrizio Celesti, Maria Fazio, Placido Bramanti, and Massimo Villari. 2017. Are next-generation sequencing tools ready for the cloud? Trends in biotechnology 35, 6 (2017), 486--489."},{"key":"e_1_3_2_1_10_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu614"},{"key":"e_1_3_2_1_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw074"},{"key":"e_1_3_2_1_12_1","unstructured":"Tinyi Chu Edward J Rice Gregory T Booth Hans H Salamanca Zhong Wang Leighton J Core Sharon L Longo Robert J Corona Lawrence S Chin John T Lis etal 2017. Chromatin run-on reveals nascent RNAs that differentiate normal and malignant brain tissue. bioRxiv (2017) 185991.  Tinyi Chu Edward J Rice Gregory T Booth Hans H Salamanca Zhong Wang Leighton J Core Sharon L Longo Robert J Corona Lawrence S Chin John T Lis et al. 2017. Chromatin run-on reveals nascent RNAs that differentiate normal and malignant brain tissue. bioRxiv (2017) 185991."},{"key":"e_1_3_2_1_13_1","doi-asserted-by":"publisher","DOI":"10.1145\/3093338.3093390"},{"key":"e_1_3_2_1_14_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1162228"},{"key":"e_1_3_2_1_15_1","volume-title":"Vivian G Cheung, W Lee Kraus, John T Lis, and Adam Siepel.","author":"Danko Charles G","year":"2015","unstructured":"Charles G Danko , Stephanie L Hyland , Leighton J Core , Andre L Martins , Colin T Waters , Hyung Won Lee , Vivian G Cheung, W Lee Kraus, John T Lis, and Adam Siepel. 2015 . Identification of active transcriptional regulatory elements from GRO-seq data. Nature methods 12, 5 (2015), 433. Charles G Danko, Stephanie L Hyland, Leighton J Core, Andre L Martins, Colin T Waters, Hyung Won Lee, Vivian G Cheung, W Lee Kraus, John T Lis, and Adam Siepel. 2015. Identification of active transcriptional regulatory elements from GRO-seq data. Nature methods 12, 5 (2015), 433."},{"key":"e_1_3_2_1_16_1","volume-title":"From genomics to metagenomics. Current opinion in biotechnology 23, 1","author":"Desai Narayan","year":"2012","unstructured":"Narayan Desai , Dion Antonopoulos , Jack A Gilbert , Elizabeth M Glass , and Folker Meyer . 2012. From genomics to metagenomics. Current opinion in biotechnology 23, 1 ( 2012 ), 72--76. Narayan Desai, Dion Antonopoulos, Jack A Gilbert, Elizabeth M Glass, and Folker Meyer. 2012. From genomics to metagenomics. Current opinion in biotechnology 23, 1 (2012), 72--76."},{"key":"e_1_3_2_1_17_1","volume-title":"BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data. Genome biology 16, 1","author":"Kartashov Andrey V","year":"2015","unstructured":"Andrey V Kartashov and Artem Barski . 2015. BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data. Genome biology 16, 1 ( 2015 ), 158. Andrey V Kartashov and Artem Barski. 2015. BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data. Genome biology 16, 1 (2015), 158."},{"key":"e_1_3_2_1_18_1","volume-title":"The human genome browser at UCSC. Genome research 12, 6","author":"Kent W James","year":"2002","unstructured":"W James Kent , Charles W Sugnet , Terrence S Furey , Krishna M Roskin , Tom H Pringle , Alan M Zahler , and David Haussler . 2002. The human genome browser at UCSC. Genome research 12, 6 ( 2002 ), 996--1006. W James Kent, Charles W Sugnet, Terrence S Furey, Krishna M Roskin, Tom H Pringle, Alan M Zahler, and David Haussler. 2002. The human genome browser at UCSC. Genome research 12, 6 (2002), 996--1006."},{"key":"e_1_3_2_1_19_1","doi-asserted-by":"publisher","DOI":"10.1109\/CCGRID.2017.121"},{"key":"e_1_3_2_1_20_1","volume-title":"Cost-effective cloud computing: a case study using the comparative genomics tool, roundup. Evolutionary Bioinformatics 6","author":"Kudtarkar Parul","year":"2010","unstructured":"Parul Kudtarkar , Todd F DeLuca , Vincent A Fusaro , Peter J Tonellato , and Dennis P Wall . 2010. Cost-effective cloud computing: a case study using the comparative genomics tool, roundup. Evolutionary Bioinformatics 6 ( 2010 ), EBO--S 6259. Parul Kudtarkar, Todd F DeLuca, Vincent A Fusaro, Peter J Tonellato, and Dennis P Wall. 2010. Cost-effective cloud computing: a case study using the comparative genomics tool, roundup. Evolutionary Bioinformatics 6 (2010), EBO--S6259."},{"key":"e_1_3_2_1_21_1","volume-title":"Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 339, 6122","author":"Kwak Hojoong","year":"2013","unstructured":"Hojoong Kwak , Nicholas J Fuda , Leighton J Core , and John T Lis . 2013. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 339, 6122 ( 2013 ), 950--953. Hojoong Kwak, Nicholas J Fuda, Leighton J Core, and John T Lis. 2013. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 339, 6122 (2013), 950--953."},{"key":"e_1_3_2_1_22_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3920"},{"key":"e_1_3_2_1_23_1","volume-title":"W1","author":"Lohse Marc","year":"2012","unstructured":"Marc Lohse , Anthony M Bolgaer , Axel Nagel , Alisdair R Fernie , John E Lunn , Mark Stitt , and Bj\u00f6rn Usadel . 2012. RobiNA: A user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic acids research 40 , W1 ( 2012 ), W622--W627. Marc Lohse, Anthony M Bolgaer, Axel Nagel, Alisdair R Fernie, John E Lunn, Mark Stitt, and Bj\u00f6rn Usadel. 2012. RobiNA: A user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic acids research 40, W1 (2012), W622--W627."},{"key":"e_1_3_2_1_24_1","doi-asserted-by":"publisher","DOI":"10.1145\/2110486.2110490"},{"key":"e_1_3_2_1_25_1","doi-asserted-by":"publisher","DOI":"10.1109\/GCE.2010.5676129"},{"key":"e_1_3_2_1_26_1","doi-asserted-by":"crossref","unstructured":"Yashar Niknafs Nicholas Molen Balaji Pandian Matthew Iyer and Arul Chinnaiyan. 2017. Bridging the gap between NGS data and its usability: cancer gene discovery through massive-scale transcriptomic analyses and development of a powerful web-tool for dissemination of these findings. (2017).  Yashar Niknafs Nicholas Molen Balaji Pandian Matthew Iyer and Arul Chinnaiyan. 2017. Bridging the gap between NGS data and its usability: cancer gene discovery through massive-scale transcriptomic analyses and development of a powerful web-tool for dissemination of these findings. (2017).","DOI":"10.1158\/1538-7445.AM2017-3038"},{"key":"e_1_3_2_1_27_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.procs.2016.05.535"},{"key":"e_1_3_2_1_28_1","volume-title":"Salmon provides fast and bias-aware quantification of transcript expression. Nature methods 14, 4","author":"Patro Rob","year":"2017","unstructured":"Rob Patro , Geet Duggal , Michael I Love , Rafael A Irizarry , and Carl Kingsford . 2017. Salmon provides fast and bias-aware quantification of transcript expression. Nature methods 14, 4 ( 2017 ), 417. Rob Patro, Geet Duggal, Michael I Love, Rafael A Irizarry, and Carl Kingsford. 2017. Salmon provides fast and bias-aware quantification of transcript expression. Nature methods 14, 4 (2017), 417."},{"key":"e_1_3_2_1_29_1","doi-asserted-by":"publisher","DOI":"10.1109\/GCE.2014.15"},{"key":"e_1_3_2_1_30_1","doi-asserted-by":"publisher","DOI":"10.1002\/cpe.3534"},{"key":"e_1_3_2_1_31_1","doi-asserted-by":"crossref","unstructured":"Sheila M Reynolds Michael Miller Phyliss Lee Kalle Leinonen Suzanne M Paquette ZackRodebaugh Abigail Hahn David L Gibbs Joseph Slagel William J Longabaugh etal 2017. The ISB Cancer Genomics Cloud: a flexible cloud-based platform for cancer genomics research. Cancer research 77 21 (2017) e7--el0.  Sheila M Reynolds Michael Miller Phyliss Lee Kalle Leinonen Suzanne M Paquette ZackRodebaugh Abigail Hahn David L Gibbs Joseph Slagel William J Longabaugh et al. 2017. The ISB Cancer Genomics Cloud: a flexible cloud-based platform for cancer genomics research. Cancer research 77 21 (2017) e7--el0.","DOI":"10.1158\/0008-5472.CAN-17-0617"},{"key":"e_1_3_2_1_32_1","volume-title":"Next-generation sequencing and epigenomics research: a hammer in search of nails. Genomics & informatics 12, 1","author":"Sarda Shrutii","year":"2014","unstructured":"Shrutii Sarda and Sridhar Hannenhalli . 2014. Next-generation sequencing and epigenomics research: a hammer in search of nails. Genomics & informatics 12, 1 ( 2014 ), 2--11. Shrutii Sarda and Sridhar Hannenhalli. 2014. Next-generation sequencing and epigenomics research: a hammer in search of nails. Genomics & informatics 12, 1 (2014), 2--11."},{"key":"e_1_3_2_1_33_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw427"},{"key":"e_1_3_2_1_34_1","doi-asserted-by":"publisher","DOI":"10.1109\/MCSE.2014.80"},{"key":"e_1_3_2_1_35_1","volume-title":"Protein secondary structure prediction using deep convolutional neural fields. Scientific reports 6","author":"Wang Sheng","year":"2016","unstructured":"Sheng Wang , Jian Peng , Jianzhu Ma , and Jinbo Xu. 2016. Protein secondary structure prediction using deep convolutional neural fields. Scientific reports 6 ( 2016 ), 18962. Sheng Wang, Jian Peng, Jianzhu Ma, and Jinbo Xu. 2016. Protein secondary structure prediction using deep convolutional neural fields. Scientific reports 6 (2016), 18962."},{"key":"e_1_3_2_1_36_1","volume-title":"Rgtsvm: Support Vector Machines on a GPU in R. arXiv preprint arXiv:1706.05544","author":"Wang Zhong","year":"2017","unstructured":"Zhong Wang , Tinyi Chu , Lauren A Choate , and Charles G Danko . 2017 . Rgtsvm: Support Vector Machines on a GPU in R. arXiv preprint arXiv:1706.05544 (2017). Zhong Wang, Tinyi Chu, Lauren A Choate, and Charles G Danko. 2017. Rgtsvm: Support Vector Machines on a GPU in R. arXiv preprint arXiv:1706.05544 (2017)."},{"key":"e_1_3_2_1_37_1","volume-title":"Identification of regulatory elements from nascent transcription using dREG. bioPxiv","author":"Wang Zhong","year":"2018","unstructured":"Zhong Wang , Tinyi Chu , Lauren A Choate , and Charles G Danko . 2018. Identification of regulatory elements from nascent transcription using dREG. bioPxiv ( 2018 ), 321539. Zhong Wang, Tinyi Chu, Lauren A Choate, and Charles G Danko. 2018. Identification of regulatory elements from nascent transcription using dREG. bioPxiv (2018), 321539."},{"key":"e_1_3_2_1_38_1","volume-title":"An Overview of the XSEDE Extended Collaborative Support Program. In International Conference on Supercomputing. Springer, 3--13","author":"Wilkins-Diehr Nancy","year":"2015","unstructured":"Nancy Wilkins-Diehr , Sergiu Sanielevici , Jay Alameda , John Cazes , Lonnie Crosby , Marlon Pierce , and Ralph Roskies . 2015 . An Overview of the XSEDE Extended Collaborative Support Program. In International Conference on Supercomputing. Springer, 3--13 . Nancy Wilkins-Diehr, Sergiu Sanielevici, Jay Alameda, John Cazes, Lonnie Crosby, Marlon Pierce, and Ralph Roskies. 2015. An Overview of the XSEDE Extended Collaborative Support Program. In International Conference on Supercomputing. Springer, 3--13."},{"key":"e_1_3_2_1_39_1","volume-title":"Deep Learning for Genomics: A Concise Overview. arXiv preprint arXiv:1802.00810","author":"Yue Tianwei","year":"2018","unstructured":"Tianwei Yue and Haohan Wang . 2018. Deep Learning for Genomics: A Concise Overview. arXiv preprint arXiv:1802.00810 ( 2018 ). Tianwei Yue and Haohan Wang. 2018. Deep Learning for Genomics: A Concise Overview. arXiv preprint arXiv:1802.00810 (2018)."},{"key":"e_1_3_2_1_40_1","volume-title":"Ivan Smirnov, Joseph F Costello, and Ting Wang.","author":"Zhou Xin","year":"2015","unstructured":"Xin Zhou , Daofeng Li , Bo Zhang , Rebecca F Lowdon , Nicole B Rockweiler , Renee L Sears , Pamela AF Madden , Ivan Smirnov, Joseph F Costello, and Ting Wang. 2015 . Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser. Nature biotechnology 33, 4 (2015), 345. Xin Zhou, Daofeng Li, Bo Zhang, Rebecca FLowdon, Nicole B Rockweiler, Renee L Sears, Pamela AF Madden, Ivan Smirnov, Joseph F Costello, and Ting Wang. 2015. Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser. Nature biotechnology 33, 4 (2015), 345."}],"event":{"name":"PEARC '18: Practice and Experience in Advanced Research Computing","acronym":"PEARC '18","location":"Pittsburgh PA USA"},"container-title":["Proceedings of the Practice and Experience on Advanced Research Computing"],"original-title":[],"link":[{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3219104.3219141","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3219104.3219141","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,18]],"date-time":"2025-06-18T02:07:06Z","timestamp":1750212426000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3219104.3219141"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,7,22]]},"references-count":40,"alternative-id":["10.1145\/3219104.3219141","10.1145\/3219104"],"URL":"https:\/\/doi.org\/10.1145\/3219104.3219141","relation":{},"subject":[],"published":{"date-parts":[[2018,7,22]]},"assertion":[{"value":"2018-07-22","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}