{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,6,19]],"date-time":"2025-06-19T04:17:55Z","timestamp":1750306675230,"version":"3.41.0"},"publisher-location":"New York, NY, USA","reference-count":34,"publisher":"ACM","license":[{"start":{"date-parts":[[2014,7,13]],"date-time":"2014-07-13T00:00:00Z","timestamp":1405209600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.acm.org\/publications\/policies\/copyright_policy#Background"}],"content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2014,7,13]]},"DOI":"10.1145\/2616498.2616551","type":"proceedings-article","created":{"date-parts":[[2014,7,11]],"date-time":"2014-07-11T12:10:42Z","timestamp":1405080642000},"page":"1-8","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Evaluating Distributed Platforms for Protein-Guided Scientific Workflow"],"prefix":"10.1145","author":[{"given":"Natasha","family":"Pavlovikj","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 66588-0115"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kevin","family":"Begcy","sequence":"additional","affiliation":[{"name":"Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sairam","family":"Behera","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 66588-0115"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Malachy","family":"Campbell","sequence":"additional","affiliation":[{"name":"Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Harkamal","family":"Walia","sequence":"additional","affiliation":[{"name":"Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jitender S.","family":"Deogun","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 66588-0115"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"320","published-online":{"date-parts":[[2014,7,13]]},"reference":[{"issue":"17","key":"e_1_3_2_1_1_1","first-page":"12","article-title":"Pegasus: Planning for Execution in Grids","volume":"20","author":"Deelman E.","unstructured":"E. Deelman , J. Blythe , Y. Gil , C. Kesselman , \" Pegasus: Planning for Execution in Grids ,\" GriPhyN technical report 20 ( 17 ): 12 -- 22 . E. Deelman, J. Blythe, Y. Gil, C. Kesselman, \"Pegasus: Planning for Execution in Grids,\" GriPhyN technical report 20(17):12--22.","journal-title":"GriPhyN technical report"},{"key":"e_1_3_2_1_2_1","volume-title":"E.Deelman, D.Gannon, M.Shields","author":"Couvares P.","year":"2007","unstructured":"P. Couvares , T. Kosar , A. Roy , Jeff Weber , K. Wenger , \" Workflow in Condor ,\" Workflows for e- Science , Editors: I. Taylor , E.Deelman, D.Gannon, M.Shields , Springer Press , January 2007 (ISBN: 1-84628-519-4). P. Couvares, T. Kosar, A. Roy, Jeff Weber, K. Wenger, \"Workflow in Condor,\" Workflows for e-Science, Editors: I.Taylor, E.Deelman, D.Gannon, M.Shields, Springer Press, January 2007 (ISBN: 1-84628-519-4)."},{"key":"e_1_3_2_1_3_1","doi-asserted-by":"publisher","DOI":"10.1155\/2005\/128026"},{"key":"e_1_3_2_1_4_1","doi-asserted-by":"publisher","DOI":"10.1145\/775047.775145"},{"key":"e_1_3_2_1_5_1","first-page":"135","article-title":"VisTrails: Enabling Interactive Multiple-View Visualizations","author":"Bavoil L.","year":"2005","unstructured":"L. Bavoil , S. P. Callahan , P. J. Crossno , J. Freire , C. E. Scheidegger , C. T. Silva , H. T. Vo , \" VisTrails: Enabling Interactive Multiple-View Visualizations .\" Proceedings of IEEE Visualization , pp. 135 -- 142 , 2005 . L. Bavoil, S. P. Callahan, P. J. Crossno, J. Freire, C. E. Scheidegger, C. T. Silva, H. T. Vo, \"VisTrails: Enabling Interactive Multiple-View Visualizations.\" Proceedings of IEEE Visualization, pp. 135--142, 2005.","journal-title":"Proceedings of IEEE Visualization"},{"key":"e_1_3_2_1_6_1","first-page":"10","article-title":"Kepler: An Extensible System for Design and Execution of Scientific Workflows","author":"Berkley C.","year":"2004","unstructured":"C. Berkley , E. Jaeger , M. Jones , B. Lud\u00e4scher . S. Mock S , \" Kepler: An Extensible System for Design and Execution of Scientific Workflows ,\" Proceedings of the The Future of Grid Data Environments, Global Grid Forum 10 , 2004 . C. Berkley, E. Jaeger, M. Jones, B. Lud\u00e4scher. S. Mock S, \"Kepler: An Extensible System for Design and Execution of Scientific Workflows,\" Proceedings of the The Future of Grid Data Environments, Global Grid Forum 10, 2004.","journal-title":"Proceedings of the The Future of Grid Data Environments, Global Grid Forum"},{"key":"e_1_3_2_1_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bth361"},{"key":"e_1_3_2_1_8_1","volume-title":"PMID 19433511","author":"Elhai J.","year":"2009","unstructured":"J. Elhai , A. Taton , J. Massar , J. K. Myers , M. Travers , J. Casey , M. Slupesky , J. Shrager , \"BioBIKE : A Web-based, programmable, integrated biological knowledge base,\" Nucleic Acids Research 37 (Web Server issue): W28--W32. doi:10.1093\/nar\/gkp354. PMC 2703918 . PMID 19433511 , 2009 . 10.1093\/nar J. Elhai, A. Taton, J. Massar, J. K. Myers, M. Travers, J. Casey, M. Slupesky, J. Shrager, \"BioBIKE: A Web-based, programmable, integrated biological knowledge base,\" Nucleic Acids Research 37 (Web Server issue): W28--W32. doi:10.1093\/nar\/gkp354. PMC 2703918. PMID 19433511, 2009."},{"key":"e_1_3_2_1_9_1","doi-asserted-by":"publisher","DOI":"10.1088\/1742-6596\/78\/1\/012057"},{"key":"e_1_3_2_1_10_1","unstructured":"Extreme Science and Engineering Discovery Environment (XSEDE). {http:\/\/www.xsede.org}.  Extreme Science and Engineering Discovery Environment (XSEDE). {http:\/\/www.xsede.org}."},{"key":"e_1_3_2_1_11_1","unstructured":"Amazon Elastic Compute Cloud (EC2). {http:\/\/aws.amazon.com\/ec2}.  Amazon Elastic Compute Cloud (EC2). {http:\/\/aws.amazon.com\/ec2}."},{"key":"e_1_3_2_1_12_1","unstructured":"FutureGrid. {http:\/\/futuregrid.org\/}.  FutureGrid. {http:\/\/futuregrid.org\/}."},{"key":"e_1_3_2_1_13_1","unstructured":"Nimbus Platform. {http:\/\/www.nimbusproject.org\/}.  Nimbus Platform. {http:\/\/www.nimbusproject.org\/}."},{"key":"e_1_3_2_1_14_1","unstructured":"Eucalyptus Open Source AWS Compatible Private Clouds. {https:\/\/www.eucalyptus.com\/}.  Eucalyptus Open Source AWS Compatible Private Clouds. {https:\/\/www.eucalyptus.com\/}."},{"key":"e_1_3_2_1_15_1","doi-asserted-by":"publisher","DOI":"10.1145\/1996109.1996114"},{"key":"e_1_3_2_1_16_1","volume-title":"May","author":"Pavlovikj N.","year":"2014","unstructured":"N. Pavlovikj , K. Begcy , S. Behera , M. Campbell , H. Walia , J. S. Deogun , \" A Comparison of a Campus Cluster and Open Science Grid Platforms for Protein-Guided Assembly using Pegasus Workflow Management System ,\" 28th IEEE International Parallel and Distributed Processing Symposium : Workshop on High Performance Computational Biology , May 2014 . N. Pavlovikj, K. Begcy, S. Behera, M. Campbell, H. Walia, J. S. Deogun, \"A Comparison of a Campus Cluster and Open Science Grid Platforms for Protein-Guided Assembly using Pegasus Workflow Management System,\" 28th IEEE International Parallel and Distributed Processing Symposium: Workshop on High Performance Computational Biology, May 2014."},{"key":"e_1_3_2_1_17_1","volume-title":"PMID 19015660","author":"Wang Z.","year":"2009","unstructured":"Z. Wang , M. Gerstein , M. Snyder , \"RNA-Seq : a revolutionary tool for transcriptomics,\" Nature Reviews Genetics 10 (1): 57--63. doi:10.1038\/nrg2484. PMC 2949280 . PMID 19015660 , 2009 . 10.1038\/nrg2484 Z. Wang, M. Gerstein, M. Snyder, \"RNA-Seq: a revolutionary tool for transcriptomics,\" Nature Reviews Genetics 10 (1): 57--63. doi:10.1038\/nrg2484. PMC 2949280. PMID 19015660, 2009."},{"key":"e_1_3_2_1_18_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.074492.107"},{"key":"e_1_3_2_1_19_1","first-page":"868","article-title":"CAP3: A DNA Sequence Assembly Program","volume":"1999","author":"Xiaoqiu H.","unstructured":"H. Xiaoqiu , M. Anup , \" CAP3: A DNA Sequence Assembly Program ,\" Genome Res. 1999 September; 9(9): 868 -- 877 . H. Xiaoqiu, M. Anup, \"CAP3: A DNA Sequence Assembly Program,\" Genome Res. 1999 September; 9(9): 868--877.","journal-title":"Genome Res."},{"key":"#cr-split#-e_1_3_2_1_20_1.1","doi-asserted-by":"crossref","unstructured":"K. Krasileva V. Buffalo P. Bailey S. Pearce S. Ayling F. Tabbita M. Soria S. Wang IWGS Consortium E. Akhunov C. Uauy J. Dubcovsky \"Separating homeologs by phasing in the tetraploid wheat transcriptome \" Genome Biology 2013 14: R66 doi:10.1186\/gb-2013-14-6-r66. 10.1186\/gb-2013-14-6-r66","DOI":"10.1186\/gb-2013-14-6-r66"},{"key":"#cr-split#-e_1_3_2_1_20_1.2","doi-asserted-by":"crossref","unstructured":"K. Krasileva V. Buffalo P. Bailey S. Pearce S. Ayling F. Tabbita M. Soria S. Wang IWGS Consortium E. Akhunov C. Uauy J. Dubcovsky \"Separating homeologs by phasing in the tetraploid wheat transcriptome \" Genome Biology 2013 14:R66 doi:10.1186\/gb-2013-14-6-r66.","DOI":"10.1186\/gb-2013-14-6-r66"},{"key":"e_1_3_2_1_21_1","first-page":"403","article-title":"Basic local alignment search tool","volume":"1990","author":"Altschul S.","unstructured":"S. Altschul , W. Gish , W. Miller , E. Myers , D. Lipman , \" Basic local alignment search tool ,\" J Mol Biol 1990 , 215: 403 -- 410 . S. Altschul, W. Gish, W. Miller, E. Myers, D. Lipman, \"Basic local alignment search tool,\" J Mol Biol 1990, 215:403--410.","journal-title":"J Mol Biol"},{"key":"e_1_3_2_1_22_1","unstructured":"Buffalo V: Blast2cap3 software. {https:\/\/github.com\/vsbuffalo\/blast2cap3\/}.  Buffalo V: Blast2cap3 software. {https:\/\/github.com\/vsbuffalo\/blast2cap3\/}."},{"key":"e_1_3_2_1_23_1","doi-asserted-by":"publisher","DOI":"10.1145\/1341811.1341822"},{"key":"e_1_3_2_1_24_1","unstructured":"Python Programming Language. {http:\/\/www.python.org\/}.  Python Programming Language. {http:\/\/www.python.org\/}."},{"key":"e_1_3_2_1_25_1","unstructured":"Biopython. {http:\/\/biopython.org\/}.  Biopython. {http:\/\/biopython.org\/}."},{"key":"e_1_3_2_1_26_1","volume-title":"October","author":"Mhashilkar P.","year":"2013","unstructured":"P. Mhashilkar , A. Tiradani , B. Holzman , K. Larson , I. Sfiligoi , M. Rynge , \" Cloud Bursting with GlideinWMS : Means to satisfy ever increasing computing needs for Scientific Workflows,\" 20th International Conference on Computing on High Energy and Nuclear Physics (CHEP) , October 2013 . P. Mhashilkar, A. Tiradani, B. Holzman, K. Larson, I. Sfiligoi, M. Rynge, \"Cloud Bursting with GlideinWMS: Means to satisfy ever increasing computing needs for Scientific Workflows,\" 20th International Conference on Computing on High Energy and Nuclear Physics (CHEP), October 2013."},{"key":"e_1_3_2_1_27_1","unstructured":"Pegasus 4.3 User Guide. {https:\/\/pegasus.isi.edu\/wms\/docs\/latest\/pegasus-user-guide.pdf\/}.  Pegasus 4.3 User Guide. {https:\/\/pegasus.isi.edu\/wms\/docs\/latest\/pegasus-user-guide.pdf\/}."},{"key":"e_1_3_2_1_28_1","unstructured":"Sandhills UNL HPC Cluster. {http:\/\/hcc.unl.edu\/sandhills\/}.  Sandhills UNL HPC Cluster. {http:\/\/hcc.unl.edu\/sandhills\/}."},{"key":"e_1_3_2_1_29_1","doi-asserted-by":"publisher","DOI":"10.1088\/1742-6596\/331\/7\/072031"},{"key":"e_1_3_2_1_30_1","unstructured":"B. Darrow \"Cycle Computing spins up 50K core Amazon cluster \" GigaOm 2012.  B. Darrow \"Cycle Computing spins up 50K core Amazon cluster \" GigaOm 2012."},{"key":"e_1_3_2_1_31_1","unstructured":"Z. Ou H. Zhuang J. K. Nurminen A. Yl\u00e4-J\u00e4\u00e4ski P. Hui \"Exploiting Hardware Heterogeneity within the Same Instance Type of Amazon EC2 \" HotCloud'12 Proceedings of the 4th USENIX conference on Hot Topics in Cloud Computing.   Z. Ou H. Zhuang J. K. Nurminen A. Yl\u00e4-J\u00e4\u00e4ski P. Hui \"Exploiting Hardware Heterogeneity within the Same Instance Type of Amazon EC2 \" HotCloud'12 Proceedings of the 4th USENIX conference on Hot Topics in Cloud Computing."},{"key":"e_1_3_2_1_32_1","unstructured":"NCBI BioProjects. {http:\/\/www.ncbi.nlm.nih.gov\/bioproject\/?term=PRJNA191053\/}.  NCBI BioProjects. {http:\/\/www.ncbi.nlm.nih.gov\/bioproject\/?term=PRJNA191053\/}."},{"key":"e_1_3_2_1_33_1","unstructured":"S. Buyske K. Vahi E. Deelman U. Peters T. Matise \"Conducting Large-Scale Imputation Studies on the Cloud \" ASHG 2013 Boston Masachuessets 2013.  S. Buyske K. Vahi E. Deelman U. Peters T. Matise \"Conducting Large-Scale Imputation Studies on the Cloud \" ASHG 2013 Boston Masachuessets 2013."}],"event":{"name":"XSEDE '14: Annual Conference of the Extreme Science and Engineering Discovery Environment","sponsor":["NSF National Science Foundation","Drexel University","Indiana University Indiana University"],"location":"Atlanta GA USA","acronym":"XSEDE '14"},"container-title":["Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment"],"original-title":[],"link":[{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/2616498.2616551","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/2616498.2616551","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,18]],"date-time":"2025-06-18T07:00:58Z","timestamp":1750230058000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/2616498.2616551"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,7,13]]},"references-count":34,"alternative-id":["10.1145\/2616498.2616551","10.1145\/2616498"],"URL":"https:\/\/doi.org\/10.1145\/2616498.2616551","relation":{},"subject":[],"published":{"date-parts":[[2014,7,13]]},"assertion":[{"value":"2014-07-13","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}