Table of Contents

• New atomic resolution insights into dynamic protein-carbohydrate interactions enabled by high-performance computingOlgun Guvench. 1 [doi]
• Low entropy data mapping for sparse iterative linear solversMahdi Esmaily Moghadam, Yuri Bazilevs, Alison L. Marsden. 2 [doi]
• Large-scale land use optimization by enhancing a scalable parallel genetic algorithm libraryYan Y. Liu, Mengyu Guo, Shaowen Wang. 3 [doi]
• Multiscale characterization of macromolecular dynamics: application to photoacitve yellow proteinMary A. Rohrdanz, Wenwei Zheng, Bradley Lambeth, Cecilia Clementi. 4 [doi]
• Attacking HIV, tuberculosis and histoplasmosis with XSEDE resourcesDavid Toth, Jimmy Franco, Charlotte Berkes. 5 [doi]
• Biomedical CyberInfrastructure challengesClaudiu Farcas, Natasha Balac, Lucila Ohno-Machado. 6 [doi]
• Low-temperature isomers of the water hexamer as predicted by q-TIP4P/F and TTM3-F potentialsVolodymyr Babin, Francesco Paesani. 7 [doi]
• An investigation of the effects of error correcting code on GPU-accelerated molecular dynamics simulationsRoss C. Walker, Robin M. Betz. 8 [doi]
• Alleviating the scaling problem of cosmological hydrodynamic simulations with HECALudwig Oser, Manisha Gajbe, Kentaro Nagamine, Greg Bryan, Jeremiah P. Ostriker, Renyue Cen. 9 [doi]
• XSEDE-enabled high-throughput lesion activity assessmentHui Zhang 0006, Michael J. Boyles, Guangchen Ruan, Huian Li, Hongwei Shen, Masatoshi Ando. 10 [doi]
• The influence of an applied heat flux on the violence of reaction of an explosive deviceMonica Hall, Jacqueline C. Beckvermit, Charles A. Wight, Todd Harman, Martin Berzins. 11 [doi]
• Referee consensus: a platform technology for nonlinear optimizationDon Krieger, Malcolm McNeil, Jinyin Zhang, Walter Schneider, Xin Li, David O. Okonkwo. 12 [doi]
• National Center for Genome Analysis support leverages XSEDE to support life science researchRichard D. LeDuc, Thomas Doak, Le-Shin Wu, Philip D. Blood, Carrie L. Ganote, Matthew Vaughn. 13 [doi]
• Optimizing the PCIT algorithm on stampede's Xeon and Xeon Phi processors for faster discovery of biological networksLars Koesterke, K. Milfeld, Matt Vaughn, Dan Stanzione, J. E. Koltes, N. T. Weeks, J. M. Reecy. 14 [doi]
• Using Lucene to index and search the digitized 1940 US censusLiana Diesendruck, Rob Kooper, Luigi Marini, Kenton McHenry. 15 [doi]
• Enabling dark energy survey science analysis with simulations on XSEDE resourcesBrandon M. S. Erickson, Raminderjeet Singh, August E. Evrard. 16 [doi]
• Making campus bridging work for researchers: a case study with mlRhoAbhinav Thota, Bernhard Haubold, Scott Michael, Thomas Doak, Sen Xu, Robert Henschel. 17 [doi]
• SocialMapExplorer: visualizing social networks of massively multiplayer online games in temporal-geographic spaceY. Dora Cai, Channing Brown, Iftekhar Ahmed, Yannick Atouba Ada, Andrew Pilny, Marshall Scott Poole. 18 [doi]
• High performance computing workflow for protein functional annotationLarissa Stanberry, Yuan Liu, Bhanu Rekepalli, Paul Giblock, Roger Higdon, William Broomall. 19 [doi]
• Exploring Twitter networks in parallel computing environmentsBo Xu, Yun Huang, Noshir S. Contractor. 20 [doi]
• The parallel system for integrating impact models and sectors (pSIMS)Joshua Elliott, David Kelly, Neil Best, Michael Wilde, Michael Glotter, Ian T. Foster. 21 [doi]
• Supercomputer assisted generation of machine learning agents for the calibration of building energy modelsJibonananda Sanyal, Joshua R. New, Richard E. Edwards. 22 [doi]
• Scalable online comparative genomics of mononucleosomes: a BigJobJack A. Smith, Yaakoub El Khamra, Melissa Romanus, Thomas C. Bishop, Pradeep Kumar Mantha, Shantenu Jha. 23 [doi]
• Fast construction of nanosecond level snapshots of financial marketsJiading Gai, Dong Ju Choi, David O'Neal, Mao Ye, Robert S. Sinkovits. 24 [doi]
• Large memory high performance computing enables comparison across human gut microbiome of patients with autoimmune diseases and healthy subjectsSitao Wu, Weizhong Li, Larry Smarr, Karen Nelson, Shibu Yooseph, Manolito Torralba. 25 [doi]
• A framework for flexible and scalable replica-exchange on production distributed CIBrian K. Radak, Tai-Sung Lee, Peng He, Melissa Romanus, Ole Weidner, Wei Dai, Emilio Gallicchio, Nan-Jie Deng, Darrin M. York, Ronald M. Levy, Shantenu Jha. 26 [doi]
• Enabling large-scale next-generation sequence assembly with BlacklightM. Brian Couger, Lenore Pipes, Philip Blood, Christopher E. Mason. 27 [doi]
• Integration of science gateways: a case study with CyberGIS and OpenTopographyAnand Padmanabhan, Choonhan Youn, Myunghwa Hwang, Yan Liu 0009, Shaowen Wang, Nancy Wilkins-Diehr, Christopher J. Crosby. 28 [doi]
• Scalable spectral transforms at petascaleDmitry Pekurovsky. 29 [doi]
• 'Spring through the gateway': deploying genomic workflows with XSEDEDavid Rhee, Joseph Hargitai, R. Brent Calder, Pilib Ó Broin, Kevin Shieh, Aaron Golden. 30 [doi]
• A neuroscience gateway: software and implementationSubhashini Sivagnanam, Vadim Astakhov, Kenneth Yoshimoto, Ted Carnevale, Maryann E. Martone, Amit Majumdar, Anita Bandrowski. 31 [doi]
• A sustainable national gateway for biological computationJames Taylor, Anton Nekrutenko, Nathan Coraor, Philip Blood, Alex Ropelewski, Zhihui Zhang, Josephine Palencia, Sergiu Sanielevici, Jared Yanovich, Robert Budden. 32 [doi]
• FluMapper: an interactive CyberGIS environment for massive location-based social media data analysisAnand Padmanabhan, Shaowen Wang, Guofeng Cao, Myunghwa Hwang, Yanli Zhao, Zhenhua Zhang, Yizhao Gao. 33 [doi]
• Experiences in building a next-generation sequencing analysis service using galaxy, globus online and Amazon web serviceRavi K. Madduri, Paul Dave, Dinanath Sulakhe, Lukasz Lacinski, Bo Liu, Ian T. Foster. 34 [doi]
• SeedMe preview: your results from disk to deviceAmit Chourasia, Mona Wong-Barnum, Michael L. Norman. 35 [doi]
• MuMMI: multiple metrics modeling infrastructure for exploring performance and power modelingXingfu Wu, Hung-Ching Chang, Shirley Moore, Valerie E. Taylor, Chun-Yi Su, Daniel Terpstra, Charles W. Lively, Kirk W. Cameron, Chee Wai Lee. 36 [doi]
• Scalasca support for MPI+OpenMP parallel applications on large-scale HPC systems based on Intel Xeon PhiBrian J. N. Wylie, Wolfgang Frings. 37 [doi]
• Exploiting MapReduce and data compression for data-intensive applicationsGuangchen Ruan, Hui Zhang 0006, Beth Plale. 38 [doi]
• Improvements of the UltraScan scientific gateway to enable computational jobs on large-scale and open-standards based cyberinfrastructuresM. Shahbaz Memon, Norbert Attig, Gary Gorbet, Lahiru Gunathilake, Morris Riedel, Thomas Lippert, Suresh Marru, Andrew S. Grimshaw, Florian Janetzko, Borries Demeler, Raminder Singh, Morris Riedel. 39 [doi]
• Embedding CIPRES science gateway capabilities in phylogenetics software environmentsMark A. Miller, Terri Schwartz, Wayne Pfeiffer. 40 [doi]
• iData: a community geospatial data sharing environment to support data-driven scienceRajesh Kalyanam, Lan Zhao, Carol X. Song, Yuet Ling Wong, Jaewoo Lee, Nelson B. Villoria. 41 [doi]
• Ab initio elasticity workflow in the VLab science gatewayPedro R. C. da Silveira, Lahiru Gunathilake, Alexander Holiday, Dave A. Yuen, M. Núñez Valdez, Renata M. Wentzcovitch. 42 [doi]
• Providing resource information to users of a national computing centerMatthew Hanlon, Warren Smith, Stephen Mock. 43 [doi]
• The XSEDE ticket system: from concept to implementationMichael Campfield, Mike Pingleton, Stephen Taylor McNally, Tabitha K. Samuel, Michael Andrew Packard, Thomas Maiden. 44 [doi]
• Hadoop deployment and performance on Gordon data intensive supercomputerMahidhar Tatineni, Jerry Greenberg, Richard Wagner, Eva Hocks, Christopher Irving. 45 [doi]
• Using XDMoD to facilitate XSEDE operations, planning and analysisThomas R. Furlani, Barry L. Schneider, Matthew D. Jones, John Towns, David L. Hart, Steven M. Gallo, Robert L. DeLeon, Charng-da Lu, Amin Ghadersohi, Ryan J. Gentner, Abani K. Patra, Gregor von Laszewski, Fugang Wang, Jeffrey T. Palmer, Nikolay Simakov. 46 [doi]
• Optimizing utilization across XSEDE platformsHaihang You, Charng-da Lu, Ziliang Zhao, Fei Xing. 47 [doi]
• Preliminary experiences with the uintah framework on Intel Xeon Phi and stampedeQingyu Meng, Alan Humphrey, John Schmidt, Martin Berzins. 48 [doi]
• OSC OnDemand: a web platform integrating access to HPC systems, web and VNC applicationsDavid E. Hudak, Thomas Bitterman, Patricia Carey, Douglas Johnson, Eric Franz, Shaun Brady, Piyush Diwan. 49 [doi]
• Comprehensive job level resource usage measurement and analysis for XSEDE HPC systemsCharng-da Lu, James C. Browne, Robert L. DeLeon, John Hammond, William Barth, Thomas R. Furlani, Steven M. Gallo, Matthew D. Jones, Abani K. Patra. 50 [doi]
• Developing a high-volume batch submission system for earthquake engineeringAnup Mohan, Thomas J. Hacker, Gregory P. Rodgers. 51 [doi]
• Adaptive latency-aware parallel resource mapping: task graph scheduling onto heterogeneous network topologyLiwen Shih. 52 [doi]
• CILogon: a federated X.509 certification authority for cyberinfrastructure logonJim Basney, Terry Fleury, Jeff Gaynor. 53 [doi]
• A Maya use case: adaptable scientific workflows with ADIOS for general relativistic astrophysicsMagdalena Slawiñska, Michael Clark, Matthew Wolf, Tanja Bode, Hongbo Zou, Pablo Laguna, Jeremy Logan, Matthew Kinsey, Scott Klasky. 54 [doi]
• NCAR storage accounting and analysis possibilitiesDavid L. Hart, Pam Gillman, Erich Thanhardt. 55 [doi]
• Enhancing the performance of scientific workflow execution in e-science environments by harnessing the standards based parameter sweep modelM. Shahbaz Memon, Morris Riedel, Sonja Holl, Morris Riedel, Bernd Schuller, Andrew S. Grimshaw. 56 [doi]
• In-situ visualization for global hybrid simulationsHoma Karimabadi, B. Loring, P. O'Leary, A. Majumdar, M. Tatineni, B. Geveci. 57 [doi]
• A high-level framework for parallelizing legacy applications for multiple platformsRitu Arora, Ejenio Capetillo, Purushotham Bangalore, Marjan Mernik. 58 [doi]
• Using Gordon to accelerate LHC scienceRick Wagner, Mahidhar Tatineni, Eva Hocks, Kenneth Yoshimoto, Scott Sakai, Michael L. Norman, Brian Bockelman, Igor Sfiligoi, Matevz Tadel, James Letts, Frank Würthwein, Lothar Bauerdick. 59 [doi]
• Providing a supported online course on parallel computingSteven I. Gordon, Jay Alameda, James Demmel, Razvan Carbunescu, Susan Mehringer. 60 [doi]
• INSTANCES: incorporating computational <u>scientific</u> thinking advances into education & science coursesPl Rubin Landau, Greg Mulder, Raquell Holmes, Sofya Borinskaya, NamHwa Kang, Cristian Bordeianu. 61 [doi]
• The condo of condosJames B. Bottum, Ruth Marinshaw, Henry Neeman, James Pepin, J. Barr von Oehsen. 62 [doi]
• Getting started with high performance computing for humanities, arts, and social scienceAlan B. Craig. 63 [doi]
• Development of undergraduate programs in computational science: panelPéter Molnár, David Toth, Rachel Vincent-Finley. 64 [doi]
• US-SOMO cluster methods: year one perspectiveEmre H. Brookes, Raminderjeet Singh, Marlon E. Pierce, Suresh Marru, Borries Demeler, Mattia Rocco. 65 [doi]
• 1000 words: advanced visualization for the humanitiesRob Turknett, Brandt M. Westing, Samuel Moore. 66 [doi]
• HPC university: getting information about computational science professional and educational resources and opportunities for engagementScott Lathrop, Ange Mason, Steven I. Gordon, Marcio Faerman. 67 [doi]
• Opposites attract: computational and quantitative outreach through artistic expressionsAmy F. Szczepanski, Christal Yost, Norman Magden, Evan Meaney, Carolyn I. Staples. 68 [doi]
• Scaling a code in the human dimensionMatthew J. Turk. 69 [doi]
• The Oklahoma cyberinfrastructure initiativeHenry Neeman, Zane Gray, Dana Brunson, Eddie Huebsch, David Horton, James Deaton, Debi Gentis. 70 [doi]
• The institute for cyber-enabled research: regional organization to promote computation in scienceDirk Colbry, Bill Punch, Wolfgang Bauer. 71 [doi]
• A tale of three outreach programs: strategic collaboration across XSEDE outreach servicesLinda Akli, Ruth Kravetz, Roger Moye. 72 [doi]
• Training, education, and outreach: raising the barLinda Akli, Samuel L. Moore, Lorna I. Rivera, Patricia J. Teller. 73 [doi]
• Human centered game design for bioinformatics and cyberinfrastructure learningDaniel Perry, Cecilia R. Aragon, Stephanie Cruz, Mette A. Peters, Jeanne Ting Chowning. 74 [doi]