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\n  \n 2018\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n Implementation of a PETSc-based Parallel General Curvilinear Coastal Ocean Model.\n \n \n \n\n\n \n Valera, M.; Garcia, M. V.; Patel, N.; Thomas, M. P.; and Castillo, J. E.\n\n\n \n\n\n\n J. Comput. Sci., Manuscript. 2018.\n \n\n\n\n
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@article{Valera2018,\nauthor = {Valera, M. and Garcia, M. V. and Patel, N. and Thomas, M. P. and Castillo, J. E.},\njournal = {J. Comput. Sci.},\nkeywords = {parallel ocean models},\ntitle = {{Implementation of a PETSc-based Parallel General Curvilinear Coastal Ocean Model}},\nvolume = {Manuscript},\nyear = {2018}\n}\n
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\n  \n 2017\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n SC16 Student Cluster Competition Challenge : Investigating the Reproducibility of Results for the ParConnect Application.\n \n \n \n\n\n \n Williams, G; Behm, G; Nguyen, T; Esparza, A; Haka, V G; Ramos, A; Wright, B; Otto, J.; Paolini, C. P.; and Thomas, M. P.\n\n\n \n\n\n\n Parallel Comput., 70: 27–24. 2017.\n \n\n\n\n
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@article{GWilliams-ParCon2017,\nauthor = {Williams, G and Behm, G and Nguyen, T and Esparza, A and Haka, V G and Ramos, A and Wright, B and Otto, J. and Paolini, C. P. and Thomas, M. P.},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Williams et al/2017/Williams et al. - 2017 - SC16 Student Cluster Competition Challenge Investigating the Reproducibility of Results for the ParConnect App.pdf:pdf},\njournal = {Parallel Comput.},\nkeywords = {MPI,message passing,parallel,performance,reproducibility},\npages = {27--24},\ntitle = {{SC16 Student Cluster Competition Challenge : Investigating the Reproducibility of Results for the ParConnect Application}},\nvolume = {70},\nyear = {2017}\n}\n
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\n \n\n \n \n \n \n \n Interfacing GCCOM within DART : A Sensitivity Analysis .\n \n \n \n\n\n \n Garcia, M.; Hoar, T.; Bailey, B.; and Thomas, M.\n\n\n \n\n\n\n In Ocean. MTS/IEEE, Monterey Bay, 2016. \n \n\n\n\n
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@inproceedings{Garcia2016a,\naddress = {Monterey Bay},\nauthor = {Garcia, Mariangel and Hoar, Timothy and Bailey, Barbara and Thomas, Mary},\nbooktitle = {Ocean. MTS/IEEE},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Garcia et al/2016/Garcia et al. - 2016 - Interfacing GCCOM within DART A Sensitivity Analysis .pdf:pdf},\ntitle = {{Interfacing GCCOM within DART : A Sensitivity Analysis .}},\nyear = {2016}\n}\n
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\n \n\n \n \n \n \n \n Nesting Nonhydrostatic GCCOM within Hydrostatic ROMS for Multiscale Coastal Ocean Modeling.\n \n \n \n\n\n \n Choboter, P. F; Garcia, M.; Cecchis, D. D.; Thomas, M.; and Walter, R. K\n\n\n \n\n\n\n In Ocean. MTS/IEEE, Monterey, 2016. \n \n\n\n\n
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@inproceedings{Choboter2016a,\naddress = {Monterey},\nauthor = {Choboter, Paul F and Garcia, Mariangel and Cecchis, Dany De and Thomas, Mary and Walter, Ryan K},\nbooktitle = {Ocean. MTS/IEEE},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Choboter et al/2016/Choboter et al. - 2016 - Nesting Nonhydrostatic GCCOM within Hydrostatic ROMS for Multiscale Coastal Ocean Modeling.pdf:pdf},\nkeywords = {nesting,nonhydrostatic,numerical models},\ntitle = {{Nesting Nonhydrostatic GCCOM within Hydrostatic ROMS for Multiscale Coastal Ocean Modeling}},\nyear = {2016}\n}\n
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\n \n\n \n \n \n \n \n Development of an Ocean Sciences Education Portal for Simulating Coastal Ocean Processes.\n \n \n \n\n\n \n Thomas, M. P.; Bucciarelli1, R.; Chao, Y.; Choboter, P.; Garcia, M.; Manjunanth, S.; and Castillo, J. E.\n\n\n \n\n\n\n In GCE15 10th Gatew. Comput. Environ. Work., pages Poster presentation, San Diego, 2016. \n \n\n\n\n
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@inproceedings{ThomasGCE2016,\naddress = {San Diego},\nauthor = {Thomas, M. P. and Bucciarelli1, R. and Chao, Y. and Choboter, P. and Garcia, M. and Manjunanth, S. and Castillo, J. E.},\nbooktitle = {GCE15 10th Gatew. Comput. Environ. Work.},\npages = {Poster presentation},\ntitle = {{Development of an Ocean Sciences Education Portal for Simulating Coastal Ocean Processes}},\nyear = {2016}\n}\n
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@article{ESu2015b,\nauthor = {Su, E. and Ko, Gene and Kumar, Sunil and Thomas, Mary P. and Garg, Rajni},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Su et al/2016/Su et al. - 2016 - Reducing Analysis Time for Identifying Drug Compounds and Screening Large Chemical Libraries with the Parallel evoQSA.pdf:pdf},\nisbn = {9788578110796},\nissn = {1098-6596},\njournal = {Manuscr. Prep.},\ntitle = {{Reducing Analysis Time for Identifying Drug Compounds and Screening Large Chemical Libraries with the Parallel evoQSAR (ParEvoQSAR) Modeling Framework.}},\nyear = {2016}\n}\n
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\n \n\n \n \n \n \n \n GCCOM_DART Ensemble Data Assimilation Analysis System for the 3D-Non-Hydrsotatic General Curvilinear Coastal Ocean Model (GCCOM).\n \n \n \n\n\n \n Garcia, M.; Hoar, T.; Thomas, M.; Bailey, B.; and Castillo, J. E.\n\n\n \n\n\n\n In Int. Counc. Ind. Appl. Math. (ICIAM 2015), Beijing, China, 2015. \n \n\n\n\n
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@inproceedings{GarciaICIAM2015,\naddress = {Beijing, China},\nauthor = {Garcia, Mariangel and Hoar, Tim and Thomas, Mary and Bailey, Barbara and Castillo, Jose E.},\nbooktitle = {Int. Counc. Ind. Appl. Math. (ICIAM 2015)},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Garcia et al/2015/Garcia et al. - 2015 - GCCOM{\\_}DART Ensemble Data Assimilation Analysis System for the 3D-Non-Hydrsotatic General Curvilinear Coastal Ocea.pdf:pdf},\nkeywords = {3d,c,curvilinear coordinates,data assimila,enakf,gccom,high resolu,hydrosta,non-,on},\ntitle = {{GCCOM{\\_}DART Ensemble Data Assimilation Analysis System for the 3D-Non-Hydrsotatic General Curvilinear Coastal Ocean Model (GCCOM)}},\nyear = {2015}\n}\n
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@inproceedings{ESU2015a,\naddress = {San Diego, CA},\nauthor = {{Eric Su, Gene M. Ko, Rajni Garg, Sunil Kumar}, And and Thomas, Mary},\nbooktitle = {Appl. Comput. Sci. Eng. Student Support},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Eric Su, Gene M. Ko, Rajni Garg, Sunil Kumar, Thomas/2015/Eric Su, Gene M. Ko, Rajni Garg, Sunil Kumar, Thomas - 2015 - Parallellization of evoQSAR Modeling Framework and Graphical User Interfac.pdf:pdf},\ntitle = {{Parallellization of evoQSAR Modeling Framework and Graphical User Interface Design using PyQt for Drug Design}},\nurl = {http://www.csrc.sdsu.edu/acsess/acsess2015/index.html},\nyear = {2015}\n}\n
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\n \n\n \n \n \n \n \n Nesting Nonhydrostatic UCOAM within Hydrostatic ROMS.\n \n \n \n\n\n \n Choboter, P.; Thomas, M. P.; and Castillo, J. E.\n\n\n \n\n\n\n In SIAM Conf. Math. Comput. Issues Geosci. (GS'15, pages Presentation., Stanford, CA, 2015. \n \n\n\n\n
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@inproceedings{Choboter2015a,\naddress = {Stanford, CA},\nauthor = {Choboter, Paul and Thomas, Mary P. and Castillo, Jose E.},\nbooktitle = {SIAM Conf. Math. Comput. Issues Geosci. (GS'15},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Choboter, Thomas, Castillo/2015/Choboter, Thomas, Castillo - 2015 - Nesting nonhydrostatic UCOAM within hydrostatic ROMS.pdf:pdf},\npages = {Presentation.},\ntitle = {{Nesting Nonhydrostatic UCOAM within Hydrostatic ROMS}},\nyear = {2015}\n}\n
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@phdthesis{ThomasDissertation2014,\naddress = {San Diego},\nauthor = {Thomas, Mary P.},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Thomas/2014/Thomas - 2014 - Parallel Implementation of the Unified Curvilinear Ocean and Atmospheric (UCOAM) Model and Supporting Computational Envi.pdf:pdf},\npages = {110},\nschool = {Claremont Graduate University and San Diego State University},\ntitle = {{Parallel Implementation of the Unified Curvilinear Ocean and Atmospheric (UCOAM) Model and Supporting Computational Environment}},\nurl = {http://sdsu-dspace.calstate.edu/handle/10211.3/120387},\nyear = {2014}\n}\n
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@inproceedings{ThomasFemTec2013,\nauthor = {Thomas, Mary and Castillo, Jose},\nbooktitle = {4th Int. Congr. Comput. Eng. Sci.},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Thomas, Castillo/2013/Thomas, Castillo - 2013 - A Cyberinfrastructure-Based Computational Environment for Unified Curvilinear Ocean Atmospheric Model ( UCOAM.pdf:pdf},\ntitle = {{A Cyberinfrastructure-Based Computational Environment for Unified Curvilinear Ocean Atmospheric Model ( UCOAM )}},\nyear = {2013}\n}\n
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\n \n\n \n \n \n \n \n Nesting ROMS and UCOAM: A Case Study in Monterey Bay.\n \n \n \n\n\n \n Thomas, M. P; Cecchis, D. D.; Choboter, P.; and Castillo, J. E.\n\n\n \n\n\n\n In Soc. Ind. Appl. Math. Annu. Meet., 2013. Computational Sciences Research Center\n \n\n\n\n
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@inproceedings{Thomas-ACSESS-2013,\nauthor = {Thomas, Mary P and Cecchis, Dany De and Choboter, Paul and Castillo, Jose E.},\nbooktitle = {Soc. Ind. Appl. Math. Annu. Meet.},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Thomas et al/2013/Thomas et al. - 2013 - Nesting ROMS and UCOAM A Case Study in Monterey Bay.pdf:pdf;:Users/mthomas/Documents/Mendeley Desktop/Thomas et al/2013/Thomas et al. - 2013 - Nesting ROMS and UCOAM A Case Study in Monterey Bay.pdf:pdf},\npublisher = {Computational Sciences Research Center},\ntitle = {{Nesting ROMS and UCOAM: A Case Study in Monterey Bay}},\nyear = {2013}\n}\n
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@techreport{More2014,\nauthor = {More, Smita and Thomas, Mary},\ninstitution = {Computational Sciences Research Center},\ntitle = {{Design and architecture of visualization services for the cyberinfrastructure web application framework}},\nurl = {http://www.csrc.sdsu.edu/research{\\_}reports.html},\nyear = {2012}\n}\n
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@inproceedings{ThomasPDPTA2012,\naddress = {Las Vegas, NV},\nauthor = {Thomas, M P and Cheng, C and More, S and Shah, H},\nbooktitle = {Int. Conf. Parallel Distrib. Process. Tech. Appl.},\ndoi = {ISBN: 1-60132-227-5},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Thomas et al/2012/Thomas et al. - 2012 - Integrating HPC Resources , Services , and Cyberinfrastructure to Develop Science Applications Using Web Applicat.pdf:pdf},\nkeywords = {CyberWeb,cyberinfrastructure,portals,pylons,python,web 2.0},\npages = {421--427},\npublisher = {CSREA Press},\ntitle = {{Integrating HPC Resources , Services , and Cyberinfrastructure to Develop Science Applications Using Web Application Frameworks}},\nvolume = {2},\nyear = {2012}\n}\n
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@inproceedings{ThomasICCSA2012a,\naddress = {Salvador de Bahia, Brazil},\nauthor = {Thomas, Mary P and Castillo, Jose E},\nbooktitle = {Int. Conf. Comput. Sci. Its Appl.},\ndoi = {10.1109/ICCSA.2012.24},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Thomas, Castillo/2012/Thomas, Castillo - 2012 - Parallelization of the 3D Unified Curvilinear Coastal Ocean Model Initial Results.pdf:pdf},\nkeywords = {3d curvilinear,computing,cyberinfrastructure,grid computing,ocean models},\npages = {88 -- 96},\ntitle = {{Parallelization of the 3D Unified Curvilinear Coastal Ocean Model: Initial Results}},\nyear = {2012}\n}\n
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@inproceedings{Thomas2010,\nauthor = {Thomas, Mary P. and Cheng, Carny and Castillo, Jose E.},\nbooktitle = {Congr. Comput. Appl. Comput. Sci.},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Thomas, Cheng, Castillo/2010/Thomas, Cheng, Castillo - 2010 - Development of a Cyberinfrastructure-based Computational Environment for the General Curvilinear Coasta.pdf:pdf},\nnumber = {Ci},\ntitle = {{Development of a Cyberinfrastructure-based Computational Environment for the General Curvilinear Coastal Ocean Model}},\nyear = {2010}\n}\n
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\n \n\n \n \n \n \n \n Improving the Performance of Thermoc hemical Computations Using Many - Task Computing Methods.\n \n \n \n\n\n \n Thomas; Cheng, C.; Bhattacharjee, S; Edwards, R. A.; and Paolini, C. P\n\n\n \n\n\n\n Technical Report Computational Sciences Research Center, 2010.\n \n\n\n\n
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@techreport{ThomasCSRC,\nauthor = {Thomas and Cheng, Carny and Bhattacharjee, S and Edwards, Robert A. and Paolini, Christopher P},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Thomas et al/2010/Thomas et al. - 2010 - Improving the Performance of Thermoc hemical Computations Using Many - Task Computing Methods.pdf:pdf},\ninstitution = {Computational Sciences Research Center},\npages = {1--12},\ntitle = {{Improving the Performance of Thermoc hemical Computations Using Many - Task Computing Methods}},\nyear = {2010}\n}\n
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\n \n\n \n \n \n \n \n Towards a General Curvilinear Ocean Model ( GCOM ) Framework.\n \n \n \n\n\n \n Thomas, M. P.; and Castillo, J. E.\n\n\n \n\n\n\n In Poster Present. Appl. Comput. Sci. Eng. Student Support Meet., 2009. \n \n\n\n\n
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@inproceedings{Thomas2009ACSESSPoster,\nauthor = {Thomas, Mary P. and Castillo, Jose E.},\nbooktitle = {Poster Present. Appl. Comput. Sci. Eng. Student Support Meet.},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Thomas, Castillo/2009/Thomas, Castillo - 2009 - Towards a General Curvilinear Ocean Model ( GCOM ) Framework.pdf:pdf},\nkeywords = {GCOM,coastal ocean model,cyberinfrastructure,cyberweb,ocean model},\ntitle = {{Towards a General Curvilinear Ocean Model ( GCOM ) Framework}},\nyear = {2009}\n}\n
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\n \n\n \n \n \n \n \n Towards a General Curvilinear Ocean Model (GCOM) Framework.\n \n \n \n\n\n \n Thomas, M.; and Castillo, J.\n\n\n \n\n\n\n In Appl. Comput. Sci. Eng. Student Support Work., volume I, 2008. \n \n\n\n\n
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@inproceedings{Thomas2008a,\nauthor = {Thomas, Mary and Castillo, Jose},\nbooktitle = {Appl. Comput. Sci. Eng. Student Support Work.},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Thomas, Castillo/2008/Thomas, Castillo - 2008 - Towards a General Curvilinear Ocean Model (GCOM) Framework.pdf:pdf},\nnumber = {block 2},\ntitle = {{Towards a General Curvilinear Ocean Model (GCOM) Framework}},\nvolume = {I},\nyear = {2008}\n}\n
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\n \n\n \n \n \n \n \n Using the Pylons Web Framework for Science Gateways.\n \n \n \n\n\n \n Thomas, M. P.\n\n\n \n\n\n\n In Grid Comput. Environ. Work., Austin, TX, 2008. \n \n\n\n\n
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@inproceedings{Thomas2008,\naddress = {Austin, TX},\nauthor = {Thomas, Mary P.},\nbooktitle = {Grid Comput. Environ. Work.},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Thomas/2008/Thomas - 2008 - Using the Pylons Web Framework for Science Gateways.pdf:pdf},\ntitle = {{Using the Pylons Web Framework for Science Gateways}},\nyear = {2008}\n}\n
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@inproceedings{Thomas2006SRB,\naddress = {La Jolla},\nauthor = {Thomas, Mary P and Bansal, Tarun and Gupta, Tushar and Seth, Akhil and Thomas, Dave},\nbooktitle = {Storage Resour. Brok. Work.},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Thomas et al/2006/Thomas et al. - 2006 - SRB Portlet Development for the Grid Portals.pdf:pdf},\ntitle = {{SRB Portlet Development for the Grid Portals}},\nyear = {2006}\n}\n
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\n \n\n \n \n \n \n \n The Open Grid Computing Enviroments Collaboration : Portlets and Services for Science Gateways.\n \n \n \n\n\n \n Alameda, J.; Christie, M.; Fox, G.; Futrelle, J.; Gannon, D.; Hategan, M.; Laszewsk, G. V.; Nacar, M. A; Pierce, M.; Roberts, E.; Severance, C.; and Thomas, M.\n\n\n \n\n\n\n Concurr. Comput. Pract. Exp., 19(6): 921–942. 2006.\n \n\n\n\n
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@article{Alameda2007,\nauthor = {Alameda, Jay and Christie, Marcus and Fox, Geoffrey and Futrelle, Joe and Gannon, Dennis and Hategan, Mihael and Laszewsk, Gregor Von and Nacar, Mehmet A and Pierce, Marlon and Roberts, Eric and Severance, Charles and Thomas, Mary},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Alameda et al/2006/Alameda et al. - 2006 - The Open Grid Computing Enviroments Collaboration Portlets and Services for Science Gateways.pdf:pdf},\njournal = {Concurr. Comput. Pract. Exp.},\nnumber = {6},\npages = {921--942},\ntitle = {{The Open Grid Computing Enviroments Collaboration : Portlets and Services for Science Gateways}},\nvolume = {19},\nyear = {2006}\n}\n
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\n \n\n \n \n \n \n \n \n Grid portal architectures for scientific applications.\n \n \n \n \n\n\n \n Thomas, M P; Burruss, J; Cinquini, L; Fox, G; Gannon, D; Gilbert, L; Laszewski, G V.; Jackson, K; Middleton, D; Moore, R; Pierce, M; Plale, B; Rajasekar, A; Regno, R; Roberts, E; Schissel, D; Seth, A; and Schroeder, W\n\n\n \n\n\n\n In J. Phys. Conf. Ser., volume 16, pages 596–600, jan 2005. \n \n\n\n\n
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@inproceedings{Thomas2005,\nauthor = {Thomas, M P and Burruss, J and Cinquini, L and Fox, G and Gannon, D and Gilbert, L and Laszewski, G Von and Jackson, K and Middleton, D and Moore, R and Pierce, M and Plale, B and Rajasekar, A and Regno, R and Roberts, E and Schissel, D and Seth, A and Schroeder, W},\nbooktitle = {J. Phys. Conf. Ser.},\ndoi = {10.1088/1742-6596/16/1/083},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Thomas et al/2005/Thomas et al. - 2005 - Grid portal architectures for scientific applications.pdf:pdf},\nissn = {1742-6588},\nmonth = {jan},\npages = {596--600},\ntitle = {{Grid portal architectures for scientific applications}},\nurl = {http://stacks.iop.org/1742-6596/16/i=1/a=083?key=crossref.729da3cd99f04421d1a9090b74d0a3f0},\nvolume = {16},\nyear = {2005}\n}\n
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\n \n\n \n \n \n \n \n Grid Portal Toolkit 3 . 0 ( GridPort ).\n \n \n \n\n\n \n Dahan, M.; Thomas, M.; Roberts, E.; Seth, A.; Urban, T.; Walling, D.; and Boisseau, J. R\n\n\n \n\n\n\n In 13th IEEE Int. Symp. High Perform. Distrib. Comput., volume 0, pages 272–273, 2004. \n \n\n\n\n
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@inproceedings{MDahan2004,\nauthor = {Dahan, Maytal and Thomas, Mary and Roberts, Eric and Seth, Akhil and Urban, Tomislav and Walling, David and Boisseau, John R},\nbooktitle = {13th IEEE Int. Symp. High Perform. Distrib. Comput.},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Dahan et al/2004/Dahan et al. - 2004 - Grid Portal Toolkit 3 . 0 ( GridPort ).pdf:pdf},\npages = {272--273},\ntitle = {{Grid Portal Toolkit 3 . 0 ( GridPort )}},\nvolume = {0},\nyear = {2004}\n}\n
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@article{Thomas2003a,\nauthor = {Thomas, M and Boisseau, J and Dahan, M and Mills, C and Mock, S and Mueller, K},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Thomas et al/2003/Thomas et al. - 2003 - Development of NPACI Grid Application Portals and Portal Web Services.pdf:pdf},\njournal = {Cluster Comput.},\npages = {177--188},\ntitle = {{Development of NPACI Grid Application Portals and Portal Web Services}},\nvolume = {6},\nyear = {2003}\n}\n
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\n \n\n \n \n \n \n \n Building Grid Computing Portals : The NPACI Grid Portal Toolkit.\n \n \n \n\n\n \n Thomas, M P; and Boisseau, J R\n\n\n \n\n\n\n In Grid Comput. Mak. Glob. Infrastruct. a Real., pages 675 – 700. 2003.\n \n\n\n\n
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@incollection{Thomas2003,\nauthor = {Thomas, M P and Boisseau, J R},\nbooktitle = {Grid Comput. Mak. Glob. Infrastruct. a Real.},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Thomas, Boisseau/2003/Thomas, Boisseau - 2003 - Building Grid Computing Portals The NPACI Grid Portal Toolkit.pdf:pdf},\nkeywords = {grid computing,ogsa,portals,portlets,toolkits,web services},\npages = {675 -- 700},\ntitle = {{Building Grid Computing Portals : The NPACI Grid Portal Toolkit}},\nyear = {2003}\n}\n
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@article{Thomas2002,\nabstract = {The implementation of multiple Grid computing portals has led us to develop a methodology for Grid portal development that facilitates rapid prototyping and building of portals. Based on the National Partnership for Advanced Computational Infrastructure (NPACI) Grid Portal Toolkit (GridPort) and the NPACI HotPage, all portals inherit interactive Grid services, share a single account and login environment, and share the infrastructure required to support and provide services used by each portal. We have demonstrated that the GridPort software can be used in production application portal environments, that the software can be configured to extend multiple sites. In this paper, we describe our experiences gained in building Grid portals and developing software for the Grid. We describe the architecture and design of the portal system, Grid services and systems employed, as well as the unique features of the system. We present descriptions of several application portals and the driving design choices. Finally, we discuss the new and emerging architecture system that being studied},\nauthor = {Thomas, Mary and Dahan, Maytal and Mueller, Kurt and Mock, Steve and Mills, Cathie and Regno, Ray},\ndoi = {10.1002/cpe.694},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Thomas et al/2002/Thomas et al. - 2002 - Application portals practice and experience.pdf:pdf},\nissn = {1532-0626},\njournal = {Concurr. Comput. Pract. Exp.},\nnumber = {13-15},\npages = {1427--1443},\ntitle = {{Application portals: practice and experience}},\nurl = {http://doi.wiley.com/10.1002/cpe.694},\nvolume = {14},\nyear = {2002}\n}\n
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\n The implementation of multiple Grid computing portals has led us to develop a methodology for Grid portal development that facilitates rapid prototyping and building of portals. Based on the National Partnership for Advanced Computational Infrastructure (NPACI) Grid Portal Toolkit (GridPort) and the NPACI HotPage, all portals inherit interactive Grid services, share a single account and login environment, and share the infrastructure required to support and provide services used by each portal. We have demonstrated that the GridPort software can be used in production application portal environments, that the software can be configured to extend multiple sites. In this paper, we describe our experiences gained in building Grid portals and developing software for the Grid. We describe the architecture and design of the portal system, Grid services and systems employed, as well as the unique features of the system. We present descriptions of several application portals and the driving design choices. Finally, we discuss the new and emerging architecture system that being studied\n
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\n \n\n \n \n \n \n \n The Perl Commodity Grid Toolkit.\n \n \n \n\n\n \n Mock, S.; Thomas, M.; and Von Lazewski, G.\n\n\n \n\n\n\n Concurr. Comput. Pract. Exp., 14(13-15): 1085–1095. 2002.\n \n\n\n\n
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@article{Mock2002Perl,\nauthor = {Mock, Stephen and Thomas, Mary and {Von Lazewski}, Gregor},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Mock, Thomas, Von Lazewski/2002/Mock, Thomas, Von Lazewski - 2002 - The Perl Commodity Grid Toolkit.pdf:pdf},\njournal = {Concurr. Comput. Pract. Exp.},\nnumber = {13-15},\npages = {1085--1095},\ntitle = {{The Perl Commodity Grid Toolkit}},\nvolume = {14},\nyear = {2002}\n}\n
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\n \n\n \n \n \n \n \n \n A batch script generator Web service for computational portals.\n \n \n \n \n\n\n \n Mock, S.; Mueller, K.; Pierce, M.; Fox, G.; and Thomas, M.\n\n\n \n\n\n\n In Proc. 11th IEEE Int. Symp. High Perform. Distrib. Comput., pages 421, 2002. IEEE Comput. Soc\n \n\n\n\n
\n\n\n\n \n \n \"APaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n  \n \n 2 downloads\n \n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@inproceedings{Mock200Batch,\nauthor = {Mock, S. and Mueller, K. and Pierce, M. and Fox, G. and Thomas, M.},\nbooktitle = {Proc. 11th IEEE Int. Symp. High Perform. Distrib. Comput.},\ndoi = {10.1109/HPDC.2002.1029951},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Mock et al/2002/Mock et al. - 2002 - A batch script generator Web service for computational portals.pdf:pdf},\nisbn = {0-7695-1686-6},\npages = {421},\npublisher = {IEEE Comput. Soc},\ntitle = {{A batch script generator Web service for computational portals}},\nurl = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=1029951},\nyear = {2002}\n}\n
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@inproceedings{Thomas2001b,\nauthor = {Thomas, M. and Mock, S. and Dahan, M. and Mueller, K. and Sutton, D. and Boisseau, J.R.},\nbooktitle = {Proc. 10th IEEE Int. Symp. High Perform. Distrib. Comput.},\ndoi = {10.1109/HPDC.2001.945191},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Thomas et al/2001/Thomas et al. - 2001 - The GridPort toolkit a system for building Grid portals.pdf:pdf},\nisbn = {0-7695-1296-8},\npages = {216--227},\npublisher = {IEEE Comput. Soc},\ntitle = {{The GridPort toolkit: a system for building Grid portals}},\nurl = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=945191},\nyear = {2001}\n}\n
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\n \n\n \n \n \n \n \n Population Pharmaccokinetic/Dynamic (PK/PD) Modeling via the World Wide Web.\n \n \n \n\n\n \n Botnen, A; Wang, X; Jelliffe, R; Thomas, M; and Hoem, N\n\n\n \n\n\n\n In Proc. Fourteenth IEEE Symp. Comput. Med. Syst., Washington, DC, 2001. IEEE Comput. Soc\n \n\n\n\n
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@inproceedings{Botnen2001,\naddress = {Washington, DC},\nauthor = {Botnen, A and Wang, X and Jelliffe, R and Thomas, M and Hoem, N},\nbooktitle = {Proc. Fourteenth IEEE Symp. Comput. Med. Syst.},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Botnen et al/2001/Botnen et al. - 2001 - Population PharmaccokineticDynamic (PKPD) Modeling via the World Wide Web.pdf:pdf},\npublisher = {IEEE Comput. Soc},\ntitle = {{Population Pharmaccokinetic/Dynamic (PK/PD) Modeling via the World Wide Web}},\nyear = {2001}\n}\n
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\n \n\n \n \n \n \n \n Message-passing computing with Java: performance evaluation and comparisons.\n \n \n \n\n\n \n Getov, V.; Lu, Q.; Thomas, M.; and Williams, M.\n\n\n \n\n\n\n In Parallel Distrib. Process. 2001. Proceedings. Ninth Euromicro Work., 2001. \n \n\n\n\n
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@inproceedings{Getov2001,\nabstract = {The development of Java has seen increasing attention as the most popular platform for distributed computing. However, despite Java's advantages in the area of portability and rapid prototyping, its efficiency is unavoidably compromised through its commitment to portability. In this paper we present performance analysis and comparisons of evaluation results for both Java and C/Fortran on three different message-passing parallel platforms-a shared memory multi-processor (Sun E4000), a Linux cluster, and a distributed memory computer (IBM SP-2). The NAS Embarrassingly Parallel and Integer Sort benchmarks were selected for this evaluation. Both the original Fortran/C codes and Java versions of these two kernels were used for obtaining the performance measurements as part of our project. The evaluation results demonstrate the feasibility of message-passing computing with Java on a wide range of computer platforms. Depending on the system and the software components installed, significant impact on the message-passing performance will have the efficiency of the native MPI library and the version of the Java platform.},\nauthor = {Getov, V. and Lu, Q. and Thomas, M. and Williams, M.},\nbooktitle = {Parallel Distrib. Process. 2001. Proceedings. Ninth Euromicro Work.},\ntitle = {{Message-passing computing with Java: performance evaluation and comparisons}},\nyear = {2001}\n}\n
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\n The development of Java has seen increasing attention as the most popular platform for distributed computing. However, despite Java's advantages in the area of portability and rapid prototyping, its efficiency is unavoidably compromised through its commitment to portability. In this paper we present performance analysis and comparisons of evaluation results for both Java and C/Fortran on three different message-passing parallel platforms-a shared memory multi-processor (Sun E4000), a Linux cluster, and a distributed memory computer (IBM SP-2). The NAS Embarrassingly Parallel and Integer Sort benchmarks were selected for this evaluation. Both the original Fortran/C codes and Java versions of these two kernels were used for obtaining the performance measurements as part of our project. The evaluation results demonstrate the feasibility of message-passing computing with Java on a wide range of computer platforms. Depending on the system and the software components installed, significant impact on the message-passing performance will have the efficiency of the native MPI library and the version of the Java platform.\n
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@inproceedings{Thomas2000-ICS00-HPJava,\naddress = {Santa Fe},\nauthor = {Thomas, Mary and Getov, Vladimir and Williams, Matthew and Whitney, Roger},\nbooktitle = {ICS 2000 HPC Java Work.},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Thomas et al/2000/Thomas et al. - 2000 - Benchmarking Java on the IBM SP-2.pdf:pdf},\ntitle = {{Benchmarking Java on the IBM SP-2}},\nyear = {2000}\n}\n
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\n \n\n \n \n \n \n \n Development of Web toolkits for computational science portals: The NPACI HotPage.\n \n \n \n\n\n \n Thomas, M.; Mock, S.; and Boisseau, J.\n\n\n \n\n\n\n In Proc. Ninth IEEE Int. Symp. High Perform. Distrib. Comput., volume 2000-Janua, pages 308–309, 2000. \n \n\n\n\n
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@inproceedings{Thomas2000IEEENinth,\nauthor = {Thomas, M. and Mock, S. and Boisseau, J.},\nbooktitle = {Proc. Ninth IEEE Int. Symp. High Perform. Distrib. Comput.},\ndoi = {10.1109/HPDC.2000.868671},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Thomas, Mock, Boisseau/2000/Thomas, Mock, Boisseau - 2000 - Development of Web toolkits for computational science portals The NPACI HotPage.pdf:pdf},\nisbn = {0769507832},\nissn = {10828907},\nkeywords = {Application software,Computer architecture,Computer interfaces,Cryptography,Distributed computing,Grid computing,High performance computing,Portals,Service oriented architecture,Web pages},\npages = {308--309},\ntitle = {{Development of Web toolkits for computational science portals: The NPACI HotPage}},\nvolume = {2000-Janua},\nyear = {2000}\n}\n
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\n  \n 1999\n \n \n (2)\n \n \n
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\n \n\n \n \n \n \n \n Investigation of Java as a High Performance Computing Language.\n \n \n \n\n\n \n Thomas, M. P. (.\n\n\n \n\n\n\n Ph.D. Thesis, San Diego State University, 1999.\n \n\n\n\n
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@phdthesis{Thomas1999ThesisJava,\nauthor = {Thomas, Mary P. (SDSU)},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Thomas/1999/Thomas - 1999 - Investigation of Java as a High Performance Computing Language.pdf:pdf},\npages = {179},\nschool = {San Diego State University},\ntitle = {{Investigation of Java as a High Performance Computing Language}},\nyear = {1999}\n}\n
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\n \n\n \n \n \n \n \n The NPACI HotPage: A Framework for Transparent Supercomputing.\n \n \n \n\n\n \n Thomas, M.; Mock, S.; and Boisseau, J.\n\n\n \n\n\n\n In Comput. Portals Work., San Francisco, CA, 1999. \n \n\n\n\n
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@inproceedings{Thomas2000Portals,\nabstract = {The NPACI HotPage framework provides users and developers with a set of simple, modular services and tools that facilitate seamless access to the NPACI grid (including high performance computers, high-speed file archival systems, and metacomputing systems such as Globus). For the end- user, a web-browser interface has been implemented that allows these resources to be viewed as an integrated system or as individual machines. When using the secure, encrypted login features, users can access their accounts directly. For the applications programmer, these simple Perl/CGI modules can be used to process HTTP requests and access resources on the grid. This paper discusses the design, architecture, and unique approach used to solve the task of providing a simple, secure, and transparent interface to users of the computational grid.},\naddress = {San Francisco, CA},\nauthor = {Thomas, Mary and Mock, Steve and Boisseau, Jay},\nbooktitle = {Comput. Portals Work.},\nfile = {:Users/mthomas/Documents/Mendeley Desktop/Thomas, Mock, Boisseau/1999/Thomas, Mock, Boisseau - 1999 - The NPACI HotPage A Framework for Transparent Supercomputing(2).pdf:pdf},\ntitle = {{The NPACI HotPage: A Framework for Transparent Supercomputing}},\nyear = {1999}\n}\n
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\n The NPACI HotPage framework provides users and developers with a set of simple, modular services and tools that facilitate seamless access to the NPACI grid (including high performance computers, high-speed file archival systems, and metacomputing systems such as Globus). For the end- user, a web-browser interface has been implemented that allows these resources to be viewed as an integrated system or as individual machines. When using the secure, encrypted login features, users can access their accounts directly. For the applications programmer, these simple Perl/CGI modules can be used to process HTTP requests and access resources on the grid. This paper discusses the design, architecture, and unique approach used to solve the task of providing a simple, secure, and transparent interface to users of the computational grid.\n
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\n  \n 1988\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n Poloidal field measurements using laser-enhanced attenuation of an energetic lithium beam.\n \n \n \n\n\n \n West, W.; Thomas, D.; and Thomas, M.\n\n\n \n\n\n\n Rev. Sci. Instrum, 58(8): 1617–1619. 1988.\n \n\n\n\n
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@article{West1988,\nauthor = {West, W.P. and Thomas, D.M. and Thomas, M.P.},\njournal = {Rev. Sci. Instrum},\nnumber = {8},\npages = {1617--1619},\ntitle = {{Poloidal field measurements using laser-enhanced attenuation of an energetic lithium beam}},\nvolume = {58},\nyear = {1988}\n}\n
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\n \n\n \n \n \n \n \n \n Characterization of Photochromic Materials as Optical Storage Media.\n \n \n \n \n\n\n \n Thomas, M P\n\n\n \n\n\n\n San Diego State University, 1985.\n \n\n\n\n
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@book{thomas1985characterization,\nauthor = {Thomas, M P},\ninstitution = {San Diego State University},\nkeywords = {laser,optical,photochromic},\npublisher = {San Diego State University},\ntitle = {{Characterization of Photochromic Materials as Optical Storage Media}},\nurl = {http://books.google.com/books?id={\\_}3DYNwAACAAJ},\nyear = {1985}\n}\n
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