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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
The workshop's discussion-oriented agenda focused on reproducibility in large-scale computational research.  ...  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).  ...  Session 1: Reproducibility in Large-Scale Computing: Where Do We Stand?  ... 
arXiv:1412.5557v2 fatcat:7hrpefkbh5agza6tpvniu2ecky

Survey and Analysis of Production Distributed Computing Infrastructures [article]

Daniel S. Katz, Shantenu Jha, Manish Parashar, Omer Rana, Jon Weissman
2012 arXiv   pre-print
This report has two objectives. First, we describe a set of the production distributed infrastructures currently available, so that the reader has a basic understanding of them.  ...  Here, the infrastructures we discuss were often designed and created with specific applications in mind, or at least specific types of applications.  ...  Moreover, as new methodologies for large-scale, data-intensive computational science (data mining, statistical analysis, etc.) continue to explode in popularity and importance, TeraGrid/XSEDE must support  ... 
arXiv:1208.2649v1 fatcat:goz6g7zkj5apzbwt4qvfrnbnlu

Survey and Analysis of Production Distributed Computing Infrastructures

Daniel S. Katz, Jon Weissman, Shantenu Jha, Omer Rana, Manish Parashar
2012 Figshare  
This report has two objectives. First, we describe a set of the production distributed infrastructures currently available, so that the reader has a basic understanding of them.  ...  Here, the infrastructures we discuss were often designed and created with specific applications in mind, or at least specific types of applications.  ...  Moreover, as new methodologies for large-scale, data-intensive computational science (data mining, statistical analysis, etc.) continue to explode in popularity and importance, TeraGrid/XSEDE must support  ... 
doi:10.6084/m9.figshare.94265.v1 fatcat:dd2q2dkj3nculd45ddwgnwbwa4

Progress towards Automated Kepler Scientific Workflows for Computer-aided Drug Discovery and Molecular Simulations

Pek U. Ieong, Jesper Sørensen, Prasantha L. Vemu, Celia W. Wong, Özlem Demir, Nadya P. Williams, Jianwu Wang, Daniel Crawl, Robert V. Swift, Robert D. Malmstrom, Ilkay Altintas, Rommie E. Amaro
2014 Procedia Computer Science  
Each co mponent is developed as a stand-alone workflow, which should allow for easy integration into larger frameworks built suiting user needs, while remaining intuitive and easy to extend.  ...  We describe the development of automated workflows that support computed -aided drug discovery (CA DD) and molecular dynamics (M D) simulat ions and are included as part of the National Bio medical Co  ...  This work used the Extreme Science and Engineering Discovery Environment (XSEDE) at San Diego Superco mputer Center (SDSC) and Texas Advanced Computing Center (TACC) using an allocation to REA with grant  ... 
doi:10.1016/j.procs.2014.05.159 pmid:29399238 pmcid:PMC5796787 fatcat:bgbwf6niunecnfqd2fthcegqle

Exchanging Best Practices and Tools for Supporting Computational and Data-Intensive Research, The Xpert Network [article]

Parinaz Barakhshan, Rudolf Eigenmann
2021 arXiv   pre-print
We focus particularly on practices that differ from those in a general software engineering context.  ...  We present best practices and tools for professionals who support computational and data intensive (CDI) research projects.  ...  ACKNOWLEDGMENTS This work was supported in part by the National Science Foundation under Award No. OAC-1833846.  ... 
arXiv:2102.09373v1 fatcat:evhj6wm7snhrnldzzdxr4nahiu

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  
Here we review the purpose for creating Jetstream, present the acceptance test results that define Jetstream's key characteristics, describe our experiences in standing up an OpenStack-based cloud environment  ...  As a multi-region deployment that operates as a single integrated system, Jetstream is proving effective in supporting modes and disciplines of research traditionally underrepresented on larger XSEDE-supported  ...  We thank reviewers of earlier versions of this report. Thanks to Dr. Winona Snapp-Childs for editorial contributions.  ... 
doi:10.1145/2949550.2949639 dblp:conf/xsede/StewartHVFCLMML16 fatcat:2y3ewhiqqfd6ffkpmnsivzefzu

Recipes 2.0: building for today and tomorrow

Rion Dooley, Matthew R. Hanlon
2014 Concurrency and Computation  
Using these components, developers can easily stand up new gateways or quickly add new functionality to existing ones.  ...  Also presented is a set of responsive front end components built on top of the iPlant Foundation API that provide the boilerplate for rapid development of lightweight science gateways using only HTML,  ...  large-scale, high-performance computational systems.  ... 
doi:10.1002/cpe.3285 fatcat:uxu7bfclmzhrbniglni2xwgoxe

Multiscale Methods for Computational RNA Enzymology [chapter]

Maria T. Panteva, Thakshila Dissanayake, Haoyuan Chen, Brian K. Radak, Erich R. Kuechler, George M. Giambaşu, Tai-Sung Lee, Darrin M. York
2015 Methods in Enzymology  
on potentially correlated protonation states of key residues and bond breaking/forming in the chemical steps of the reaction.  ...  The multi-dimensional "problem space" of RNA catalysis includes both local and global conformational rearrangements, changes in the ion atmosphere around nucleic acids and metal ion binding, dependence  ...  Computational resources utilized for this research include the Extreme Science and Engineering Discovery Environment (XSEDE), NSF grant number OCI-1053575, the Blue Waters super computer, NSF grant numbers  ... 
doi:10.1016/bs.mie.2014.10.064 pmid:25726472 pmcid:PMC4739856 fatcat:6sulkyhhtvhqjllibkk7qvlrsu

29th Annual Computational Neuroscience Meeting: CNS*2020

2020 BMC Neuroscience  
Investigations of this question have, to date, focused largely on deep neural networks trained using supervised learning, in tasks such as image classification.  ...  K2 A new computational framework for understanding vision in our brain Zhaoping Li Correspondence: Zhaoping Li (li.zhaoping@tuebingen.mpg.de) BMC Neuroscience 2020, 21(Suppl 1):K2 Visual attention selects  ...  Acknowledgments: The research reported here was supported, in part, by NSF grant #1544383 and in part by AFOSR grant #FA9550-16-1-0410.  ... 
doi:10.1186/s12868-020-00593-1 pmid:33342424 fatcat:edosycf35zfifm552a2aogis7a

27th Annual Computational Neuroscience Meeting (CNS*2018): Part One

2018 BMC Neuroscience  
Acknowledgements We thank Ramón Huerta for his useful discussions on this work. This research was supported by the Spanish Government projects TIN2014-54580-R and TIN2017-84452-R.  ...  Gutzen for fruitful discussions.  ...  Changes of peak gamma frequency and power ratio were readily reproduced by our computational model, accounting for several experimental findings reported in the literature.  ... 
doi:10.1186/s12868-018-0452-x pmid:30373544 pmcid:PMC6205781 fatcat:xv7pgbp76zbdfksl545xof2vzy

Sustained Software for Cyberinfrastructure

Craig A. Stewart, William K. Barnett, Eric A. Wernert, Julie A. Wernert, Von Welch, Richard Knepper
2015 Proceedings of the 1st Workshop on The Science of Cyberinfrastructure Research, Experience, Applications and Models - SCREAM '15  
Reliable software that provides needed functionality is clearly essential for an effective distributed cyberinfrastructure (CI) that supports comprehensive, balanced, and flexible distributed CI.  ...  The purpose of this study was to understand what factors lead to software projects being well sustained over the long run, focusing on software created with funding from the US National Science Foundation  ...  This research is based upon work supported in part by the National Science Foundation under Award No. 1147606 and builds on work supported by NSF awards 1002526 & 0829462.  ... 
doi:10.1145/2753524.2753533 dblp:conf/hpdc/StewartBWWWK15 fatcat:ncayerm5fzh5pfoqcgg2kbaxia

Introducing a New Client/Server Framework for Big Data Analytics with the R Language

Drew Schmidt, Wei-Chen Chen, George Ostrouchov
2016 Proceedings of the XSEDE16 on Diversity, Big Data, and Science at Scale - XSEDE16  
To handle server side computations, we use our established pbdR packages for large scale distributed computing.  ...  Historically, large scale computing and interactivity have been at odds. This is a particularly sore spot for data analytics applications, which are typically interactive in nature.  ...  Harnessing Scalable Libraries for Statistical Computing on Modern Architectures and Bringing Statistics to Large Scale Computing funded by the National Science Foundation Division of Mathematical Sciences  ... 
doi:10.1145/2949550.2949651 dblp:conf/xsede/SchmidtCO16 fatcat:fgvcwmmiofatjpefvg6uwdi3aq

Nucleic acid reactivity: Challenges for next-generation semiempirical quantum models

Ming Huang, Timothy J. Giese, Darrin M. York
2015 Journal of Computational Chemistry  
Further, a recently developed linear-scaling "modified divide-and-conquer" model exhibits the most accurate results for binding energies of both hydrogen bonded and stacked nucleobase dimers.  ...  AM1/d-PhoT and DFTB3-3ob/OPhyd reproduce the MP2 potential energy surfaces of 6 associative RNA phosphoryl transfer model reactions reasonably well.  ...  Acknowledgement The authors are grateful for financial support provided by the National Institutes of Health (GM62248).  ... 
doi:10.1002/jcc.23933 pmid:25943338 pmcid:PMC4760688 fatcat:gjcfmmxotjcbbci6td76iaeoc4

Properties of galaxies reproduced by a hydrodynamic simulation

M. Vogelsberger, S. Genel, V. Springel, P. Torrey, D. Sijacki, D. Xu, G. Snyder, S. Bird, D. Nelson, L. Hernquist
2014 Nature  
It yields a reasonable population of ellipticals and spirals, reproduces the distribution of galaxies in clusters and statistics of hydrogen on large scales, and at the same time the metal and hydrogen  ...  content of galaxies on small scales.  ...  Looking ahead Although our simulation provides a significant step forward in modelling galaxy formation by reproducing simultaneously many disparate observations on large and small scales, there are still  ... 
doi:10.1038/nature13316 pmid:24805343 fatcat:2n4oigxgavbpbewd5sdwyl3e6m

Community Organizations: Changing the Culture in Which Research Software Is Developed and Sustained

Daniel S. Katz, Lois Curfman McInnes, David E. Bernholdt, Abigail Cabunoc Mayes, Neil P. Chue Hong, Jonah Duckles, Sandra Gesing, Michael A. Heroux, Simon Hettrick, Rafael C. Jimenez, Marlon Pierce, Belinda Weaver (+1 others)
2019 Computing in science & engineering (Print)  
Moreover, challenges in scientific software are expanding due to disruptive changes in computer hardware, increasing scale and complexity of data, and demands for more complex simulations involving multiphysics  ...  Software is the key crosscutting technology that enables advances in mathematics, computer science, and domain-specific science and engineering to achieve robust simulations and analysis for science, engineering  ...  IDEAS, BSSw, and xSDK acknowledge support from the Exascale Computing Project (17-SC-20-SC), a collaborative effort of the U.S.  ... 
doi:10.1109/mcse.2018.2883051 fatcat:jmemakin4bbtbb3sm2wbkfnlha
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