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National Center for Genome Analysis support leverages XSEDE to support life science research

Richard D. LeDuc, Thomas Doak, Le-Shin Wu, Philip D. Blood, Carrie L. Ganote, Matthew Vaughn
2013 Proceedings of the Conference on Extreme Science and Engineering Discovery Environment Gateway to Discovery - XSEDE '13  
The National Center for Genome Analysis Support (NC-GAS) is a response to the concern that NSF-funded life scientists were underutilizing the national cyberinfrastructure.  ...  to domain scientists unfamiliar with next generation DNA sequence data analysis.  ...  On September 15, 2011, Indiana University (IU) received three years of support to establish the National Center for Genome Analysis Support [3] to help NSF-funded life scientists leverage the national  ... 
doi:10.1145/2484762.2484790 dblp:conf/xsede/LeDucDWBGV13 fatcat:rrkedkv6kzg3jhwwwjoefqtnhu

Leveraging the national cyberinfrastructure for biomedical research

Richard LeDuc, Matthew Vaughn, John M Fonner, Michael Sullivan, James G Williams, Philip D Blood, James Taylor, William Barnett
2014 JAMIA Journal of the American Medical Informatics Association  
Specialized web portals, support centers, and virtual organizations can be constructed on these resources to meet defined computational challenges, specifically for genomics.  ...  In the USA, the national cyberinfrastructure refers to a system of research supercomputer and other IT facilities and the high speed networks that connect them.  ...  Contributors RL manages the National Center for Genome Analysis Support; MV manages Life Science Computing at the Texas Advanced Computing Center, and JMF is a Research Associate there; MS is the Associate  ... 
doi:10.1136/amiajnl-2013-002059 pmid:23964072 pmcid:PMC3932465 fatcat:mla5vg3t4vcjnno5igcwnxxmrq

Jetstream

Craig A. Stewart, George Turner, Matthew Vaughn, Niall I. Gaffney, Timothy M. Cockerill, Ian Foster, David Hancock, Nirav Merchant, Edwin Skidmore, Daniel Stanzione, James Taylor, Steven Tuecke
2015 Proceedings of the 2015 XSEDE Conference on Scientific Advancements Enabled by Enhanced Cyberinfrastructure - XSEDE '15  
Jetstream will be the first production cloud resource supporting general science and engineering research within the XD ecosystem.  ...  to use this new system.  ...  • polar science: Tools for accessing data from the National Snow and Ice Data Center [19]. • network science: Open-source tools for network analysis [20].  ... 
doi:10.1145/2792745.2792774 dblp:conf/xsede/StewartCFHMSSTT15 fatcat:nbppel4vpfc23p33ccy3jcrvqu

Building a Shared Resource HPC Center Across University Schools and Institutes: A Case Study [article]

Glen MacLachlan, Jason Hurlburt, Marco Suarez, Kai Leung Wong, William Burke, Terrence Lewis, Andrew Gallo, Jaroslav Flidr, Raoul Gabiam, Janis Nicholas, Brian Ensor
2020 arXiv   pre-print
We discuss the challenges and obstacles encountered planning and establishing a first-time high performance computing center at the university level and present a set of solutions that will be useful for  ...  any university developing a fledgling high performance computing center.  ...  We gratefully acknowledge Sean Connolly and Warren Santner who did much of the work to pioneer the implementation of a HPCC at The George Washington University. ADDITIONAL AUTHORS  ... 
arXiv:2003.13629v2 fatcat:6iq5biyqdbgsdhks4zbgc4ig4a

Rockhopper, a true HPC system built with cloud concepts

Richard Knepper, Barbara Hallock, Craig Stewart, Matthew Link, Matthew Jacobs
2013 2013 IEEE International Conference on Cluster Computing (CLUSTER)  
the way up through large national resources.  ...  Furthermore, the lack of location information provided to the user and the shared nature of the systems use may create risk for users of the system, in the instance that their data is moved to an unknown  ...  This system is also a major component of Indiana University's campus bridging initiatives, interoperating with initiatives by XSEDE and the 978-1-4799-0898-1/13/$31.00 c 2013 IEEE National Center for Genome  ... 
doi:10.1109/cluster.2013.6702658 dblp:conf/cluster/KnepperHSLJ13 fatcat:jm6skp63tbcgfgolakuklsffku

Standing Together for Reproducibility in Large-Scale Computing: Report on reproducibility@XSEDE [article]

Doug James, Nancy Wilkins-Diehr, Victoria Stodden, Dirk Colbry, Carlos Rosales, Mark Fahey, Justin Shi, Rafael F. Silva, Kyo Lee, Ralph Roskies, Laurence Loewe, Susan Lindsey, Rob Kooper (+36 others)
2015 arXiv   pre-print
support reproducible research; and (2) individual researchers should conduct each experiment as though someone will replicate that experiment.  ...  This is the final report on reproducibility@xsede, a one-day workshop held in conjunction with XSEDE14, the annual conference of the Extreme Science and Engineering Discovery Environment (XSEDE).  ...  This rapidly maturing tool, currently deployed on production systems at the National Institute for Computational Sciences (NICS) and the Texas Advanced Computing Center (TACC), is available for beta testing  ... 
arXiv:1412.5557v2 fatcat:7hrpefkbh5agza6tpvniu2ecky

Jetstream

Craig A. Stewart, Daniel C. Stanzione, James Taylor, Edwin Skidmore, David Y. Hancock, Matthew Vaughn, Jeremy Fischer, Tim Cockerill, Lee Liming, Nirav Merchant, Therese Miller, John Michael Lowe
2016 Proceedings of the XSEDE16 on Diversity, Big Data, and Science at Scale - XSEDE16  
Already, researchers in biology, network science, economics, earth science, and computer science have used Jetstream to perform researchmuch of it research in the "long tail of science."  ...  Jetstream offers unique capability within the XSEDE-supported US national cyberinfrastructure, delivering interactive virtual machines (VMs) via the Atmosphere interface developed by the University of  ...  This material is based upon work supported in part by the National Science Foundation under Award 1445604.  ... 
doi:10.1145/2949550.2949639 dblp:conf/xsede/StewartHVFCLMML16 fatcat:2y3ewhiqqfd6ffkpmnsivzefzu

iMicrobe: Tools and data-dreaiven discovery platform for the microbiome sciences

Ken Youens-Clark, Matt Bomhoff, Alise J Ponsero, Elisha M Wood-Charlson, Joshua Lynch, Illyoung Choi, John H Hartman, Bonnie L Hurwitz
2019 GigaScience  
Findings The iMicrobe platform brings together analysis tools and microbiome datasets by leveraging National Science Foundation–supported cyberinfrastructure and computing resources from CyVerse, Agave  ...  The primary purpose of iMicrobe is to provide users with a freely available, web-based platform to (1) maintain and share project data, metadata, and analysis products, (2) search for related public datasets  ...  This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant No. ACI-1548562.  ... 
doi:10.1093/gigascience/giz083 pmid:31289831 pmcid:PMC6615980 fatcat:cq4cvvg5mjfr3fzbtvt2yangwq

The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences

Nirav Merchant, Eric Lyons, Stephen Goff, Matthew Vaughn, Doreen Ware, David Micklos, Parker Antin
2016 PLoS Biology  
The iPlant Collaborative provides life science research communities access to comprehensive, scalable, and cohesive computational infrastructure for data management; identity management; collaboration  ...  computational tools and analysis workflows, allowing the broader community to easily use and reuse those data and computational analyses.  ...  These projects have allowed iPlant to rapidly deploy and extend its cyberinfrastructure.  ... 
doi:10.1371/journal.pbio.1002342 pmid:26752627 pmcid:PMC4709069 fatcat:uwhpaj2ryvewlgfyljkx2sjdzm

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

Stephen A. Goff, Matthew Vaughn, Sheldon McKay, Eric Lyons, Ann E. Stapleton, Damian Gessler, Naim Matasci, Liya Wang, Matthew Hanlon, Andrew Lenards, Andy Muir, Nirav Merchant (+53 others)
2011 Frontiers in Plant Science  
The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of  ...  new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure  ...  The TNRS is a collaborative effort between iPlant and the Botanical Information and Ecology Network (BIEN), a working group supported by the National Center for Ecological Analysis and Synthesis (Reichman  ... 
doi:10.3389/fpls.2011.00034 pmid:22645531 pmcid:PMC3355756 fatcat:nwkuqfhsorddrppjjzs6oz76ci

A Vision for Collaborative Training Infrastructure for Bioinformatics

Jason Williams
2016 Figshare  
Given thetransformative potential of biology and medicine as full-fledged data sciences, more support is needed to organize, amplify, and assess these efforts and their impacts.  ...  This is a vision paper based on content pretested at an NSF Northeast Big Data Innovation Hub meeting on data science learning in biomedical/health topics.Abstract: prepares researchers to effectively  ...  ACKNOWLEDGMENTS The authors thank Lindsay Barone, Jonah Duckles and Greg Wilson for helpful comments and corrections.  ... 
doi:10.6084/m9.figshare.3807723 fatcat:hdvs4p6mdnaxdg567x57qj7v4e

Cyberinfrastructure: Applications and challenges

Qiuhui Tong, Bo Yuan, Xiu Li
2014 2014 International Conference on Smart Computing  
An in-depth analysis is also conducted to reveal the key functions and desired features that can be expected from modern CI systems.  ...  This paper presents a comprehensive review of Cyberinfrastructure (CI), an emerging collaborative research environment, including its representative applications in four science communities around the  ...  ACKNOWLEDGMENT This paper is supported by National Natural Science Foundation of China (NSFC, Project No.: 71171121).  ... 
doi:10.1109/smartcomp.2014.7043842 dblp:conf/smartcomp/TongYL14 fatcat:qicaif2z2jbydomotj3g2vubeq

A phylogenetically novel cyanobacterium most closely related to Gloeobacter

Christen L. Grettenberger, Dawn Y. Sumner, Kate Wall, C. Titus Brown, Jonathan A. Eisen, Tyler J. Mackey, Ian Hawes, Guillaume Jospin, Anne D. Jungblut
2020 The ISME Journal  
The MAG of A. vandensis contains homologs of most genes necessary for oxygenic photosynthesis including key reaction center proteins.  ...  However, only two species with published genomes are known to occupy this phylogenetic space, both within the genus Gloeobacter.  ...  Salary support for CG was provided by the Massachusetts Institute of Technology node of the NASA Astrobiology Institute and the National Science Foundation (grant 1745341).  ... 
doi:10.1038/s41396-020-0668-5 pmid:32424249 fatcat:cx2f7xgq4be4flb4k6tf5vmh4u

The U.S. High-Performance Computing Consortium in the Fight Against COVID-19

James J. Hack, Michael E. Papka, James J. Hack, Michael E. Papka
2020 Computing in science & engineering (Print)  
U.S. computing leaders, including Department of Energy National Laboratories, have partnered with universities, government agencies, and the private sector to research responses to COVID-19, providing  ...  For HPC users, these leadership machines will drive the AI to accelerate the discovery of promising treatments, enable at-scale simulations to understand the virus's protein structure and attack mechanisms  ...  pipeline, leveraging Theta for highspeed on-demand analysis.  ... 
doi:10.1109/mcse.2020.3019744 fatcat:3lrzhjxv2ncvrcrme5f5zysk7y

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

Enis Afgan, Dannon Baker, Bérénice Batut, Marius van den Beek, Dave Bouvier, Martin Čech, John Chilton, Dave Clements, Nate Coraor, Björn A Grüning, Aysam Guerler, Jennifer Hillman-Jackson (+8 others)
2018 Nucleic Acids Research  
Started in 2005, Galaxy continues to focus on three key challenges of data-driven biomedical science: making analyses accessible to all researchers, ensuring analyses are completely reproducible, and making  ...  The Galaxy community has led an effort to create numerous high-quality tutorials focused on common types of genomic analyses.  ...  FUNDING National Human Genome Research Institute, National Institutes of Health [HG006620, HG005133, HG004909 and HG005542]; NSF [DBI 0543285, 0850103 and 1661497]; Huck Institutes for the Life Sciences  ... 
doi:10.1093/nar/gky379 pmid:29790989 pmcid:PMC6030816 fatcat:bfp64x6qizahzjj5yoybdkufku
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