Presentations
Permanent link for this collectionhttps://hdl.handle.net/2022/14534
Browse
Browsing Presentations by Issue Date
Now showing 1 - 20 of 87
- Results Per Page
- Sort Options
Item National Center for Genome Analysis Support (Poster)(2012) Doak, Thomas G.; Wu, Le-Shin; Stewart, Craig A.; Henschel, Robert; Barnett, William K.Item A Nation-Wide Area Networked File System for Very Large Scientific Data(2012-04-25) Barnett, William K.; LeDuc, RichardSequencing is creating analytical problems that cannot be solved at sequencing centers or labs. Bioinformatics support, storage, data transfer, and computation all needed to do the science. NCGAS provides a model of a scaled infrastructure for biologists who cannot become bioinformaticians to accomplish their research.Item High Performance Data Management and Computational Architectures for Genomics Research at National and International Scales(2012-06-07) Barnett, William K.; LeDuc, RichardSummary: Changing genomics analytical needs; NCGAS and its mission; NCGAS cyberinfrastructure; the 100 Gigabit demonstration; scaling genomics analysis; the NCGAS research model; and outcomes for life sciences researchItem The National Center for Genome Analysis Support and Galaxy(2012-07-27) LeDuc, Richard D.; Barnett, William K.The National Center for Genome Analysis Support is an NSF funded resource designed to supply bioinformatic support and computational infrastructure to genomics projects requiring large RAM computational resources – specifically de novo sequence assembly. We are developing a national scale infrastructure to support biological researchers that will use Galaxy to interface between the biologists and the cyberinfrastructure. The ability of NCGAS to assist with bioinformatic software optimization was recently demonstrated by our assistance in optimizing the runtime performance of Trinity resulting in over 3x speed improvement.Item The National Center for Genome Analysis Support (Poster)(2012-09) Doak, Thomas G.; LeDuc, Richard; Wu, Le-Shin; Stewart, Craig A.; Henschel, Robert; Barnett, William K.Item Careers in Computing and Science(2012-09-27) LeDuc, Richard D.Item Genomics, Transcriptomics, and Proteomics: Engaging Biologists(2012-10-08) LeDuc, Richard D.Item The National Center for Genome Analysis and Support(2013-01-13) LeDuc, Richard; Barnett, William K.Item Statistical Consideration for Identification and Quantification in Top-Down Proteomics(2013-01-27) LeDuc, RichardItem Galaxy based BLAST submission to distributed national high throughput computing resources(2013-03) Hayashi, Soichi; Gesing, Sandra; Quick, Rob; Teige, Scott; Ganote, Carrie; Wu, Le-shin; Prout, ElizabethTo assist the bioinformatic community in leveraging the national cyberinfrastructure, the National Center for Genomic Analysis Support (NCGAS) along with Indiana University's High Throughput Computing (HTC) group have engineered a method to use the Galaxy to submit BLAST jobs to the Open Science Grid (OSG). OSG is a collaboration of resource providers that utilize opportunistic cycles at more than 100 universities and research centers in the US. BLAST jobs make a significant portion of the research conducted on NCGAS resources, moving jobs that are conducive to an HTC environment to the national cyberinfrastructure would alleviate load on resources at NCGAS and provide a cost effective solution for getting more cycles to reduce the unmet needs of bioinformatic researchers. To this point researchers have tackled this issue by purchasing additional resources or enlisting collaborators doing the same type of research, while HTC experts have focused on expanding the number of resources available to historically HTC friendly science workflows. In this paper, we bring together expertise from both areas to address how a bioinformatics researcher using their normal interface, Galaxy, can seamlessly access the OSG which routinely supplies researchers with millions of compute hours daily. Efficient use of these results will supply additional compute time to researcher and help provide a yet unmet need for BLAST computing cycles.Item NCGAS (Poster at AMIA Translational Bioinformatics Summit)(2013-03) Barnett, William K.; LeDuc, Richard D.Item Consequences of whole genome duplication in Paramecium sps.(2013-05) McGrath, C.L.; Gout, J.F.; Johri, P.; Doak, T.G.; Lynch, M.Item Next Generation Cyberinfrastructures for Next Generation Sequencing and Genome Science(2013-06-05) Barnett, William K.; LeDuc, RichardItem Using Prior Knowledge to Improve Scoring in High-Throughput Top-Down Proteomics Experiments(2013-06-08) LeDuc, Richard D.; Wu, Le-ShinItem Leveraging the National Cyberinfrastructure for Top Down Mass Spectrometry(2013-06-08) LeDuc, Richard D.Item Intro to Bioinformatics - Assembling a Transcriptome(2013-06-13) Ganote, Carrie L.; Doak, ThomasItem Optimizing the National Cyberinfrastructure for Lower Bioinformatic Costs: Making the Most of Resources for Publicly Funded Research(2013-06-20) Barnett, William K.; LeDuc, Richard D.Overviews of NCGAS mission, cyberinfrastructure, and server-on-demand resources and of XSEDE for larger-scale resources.Item Consequences of whole genome duplication in Paramecium sps.(2013-07) McGrath, C.L.; Gout, J.F.; Johri, P.; Doak, T.G.; Lynch, M.Item National Center for Genome Analysis Support Leverages XSEDE Resources to Support Life Scientists(2013-07-23) Barnett, William K.; LeDuc, Richard D.Item Intro to Using Galaxy for Bioinformatics(2013-09-17) Ganote, Carrie L.; Doak, Thomas