research-article

Building an environment to facilitate discoveries for plant sciences

Authors:

Andrew Lenards,

Nirav Merchant,

Dan StanzioneAuthors Info & Claims

GCE '11: Proceedings of the 2011 ACM workshop on Gateway computing environments

Pages 51 - 58

https://doi.org/10.1145/2110486.2110494

Published: 18 November 2011 Publication History

Abstract

The iPlant Collaborative is an NSF-funded cyberinfrastructure (CI) effort directed towards the plant sciences community. This paper enumerates the key concepts, middleware, tools, and extensions that create the unique capabilities of the iPlant Discovery Environment (DE) that provide access to our CI. The DE is a rich web-based application that brings flexible CI capabilities to a wide audience affiliated with the plant sciences, from computational biologists, bioinformaticians, applications developers, to bench biologists.

The inherent interdisciplinary nature of plant sciences research produces diverse and complex data products that range from molecular sequences to satellite imagery as part of the discovery life cycle. With the constant creation of novel analysis algorithms, the advent and spread of large data repositories, and the need for collaborative data analysis, marshaling resources to effectively utilize these capabilities necessitates a highly flexible and scalable approach for implementing underlying CI.

The iPlant infrastructure simultaneously supports multiple interdisciplinary projects providing essential features found in traditional science gateways as well as highly customized direct access to its underlying frameworks through use of APIs (Application Programming Interfaces). This allows the community to develop de novo applications. This approach allows us to serve broad community needs while providing flexible, secure, and creative utilization of our platform that is based on best practices and that leverages established computational resources.

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Cited By

Dooley RBrandt SFonner JSanielevici S(2018)The Agave PlatformProceedings of the Practice and Experience on Advanced Research Computing: Seamless Creativity10.1145/3219104.3219129(1-8)Online publication date: 22-Jul-2018
https://dl.acm.org/doi/10.1145/3219104.3219129
Shahand Svan Kampen AOlabarriaga SJha SKatz DWeissman J(2015)Science Gateway CanvasProceedings of the 1st Workshop on The Science of Cyberinfrastructure: Research, Experience, Applications and Models10.1145/2753524.2753527(45-52)Online publication date: 16-Jun-2015
https://dl.acm.org/doi/10.1145/2753524.2753527
Jaghoori MShahand SOlabarriaga S(2015)Processing Manager for Science GatewaysProceedings of the 2015 7th International Workshop on Science Gateways10.1109/IWSG.2015.9(1-7)Online publication date: 3-Jun-2015
https://dl.acm.org/doi/10.1109/IWSG.2015.9
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Index Terms

Building an environment to facilitate discoveries for plant sciences
1. Software and its engineering
  1. Software notations and tools
    1. Development frameworks and environments
      1. Integrated and visual development environments

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cover image ACM Conferences

GCE '11: Proceedings of the 2011 ACM workshop on Gateway computing environments

November 2011

80 pages

ISBN:9781450311236

DOI:10.1145/2110486

General Chairs:
Rion Dooley
Texas Advanced Computing Center
,
Sandro Fiore
Euro-Mediterranean Centre for Climate Change
,
Mark L. Green
Tech-X Corporation
,
Cameron Kiddle
University of Calgary
,
Suresh Marru
Indiana University
,
Marlon E. Pierce
Indiana University
,
Mary Thomas
San Diego State University
,
Nancy Wilkins-Diehr
San Diego Supercomputer Center

Copyright © 2011 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Publication History

Published: 18 November 2011

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SC '11: International Conference for High Performance Computing, Networking, Storage and Analysis

November 18, 2011

Washington, Seattle, USA

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Cited By

Dooley RBrandt SFonner JSanielevici S(2018)The Agave PlatformProceedings of the Practice and Experience on Advanced Research Computing: Seamless Creativity10.1145/3219104.3219129(1-8)Online publication date: 22-Jul-2018
https://dl.acm.org/doi/10.1145/3219104.3219129
Shahand Svan Kampen AOlabarriaga SJha SKatz DWeissman J(2015)Science Gateway CanvasProceedings of the 1st Workshop on The Science of Cyberinfrastructure: Research, Experience, Applications and Models10.1145/2753524.2753527(45-52)Online publication date: 16-Jun-2015
https://dl.acm.org/doi/10.1145/2753524.2753527
Jaghoori MShahand SOlabarriaga S(2015)Processing Manager for Science GatewaysProceedings of the 2015 7th International Workshop on Science Gateways10.1109/IWSG.2015.9(1-7)Online publication date: 3-Jun-2015
https://dl.acm.org/doi/10.1109/IWSG.2015.9
Wang LBuren PWare D(2015)Architecting a Distributed Bioinformatics Platform with iRODS and iPlant Agave APIProceedings of the 2015 International Conference on Computational Science and Computational Intelligence (CSCI)10.1109/CSCI.2015.121(420-423)Online publication date: 7-Dec-2015
https://dl.acm.org/doi/10.1109/CSCI.2015.121
LeDuc RVaughn MFonner JSullivan MWilliams JBlood PTaylor JBarnett W(2014)Leveraging the national cyberinfrastructure for biomedical researchJournal of the American Medical Informatics Association10.1136/amiajnl-2013-00205921:2(195-199)Online publication date: 1-Mar-2014
https://doi.org/10.1136/amiajnl-2013-002059
Wang LWare DLushbough CMerchant NStein L(2014)A genome‐wide association study platform built on iPlant cyber‐infrastructureConcurrency and Computation: Practice and Experience10.1002/cpe.323627:2(420-432)Online publication date: 6-Mar-2014
https://doi.org/10.1002/cpe.3236
Elliott JKelly DBest NWilde MGlotter MFoster IWilkins-Diehr N(2013)The parallel system for integrating impact models and sectors (pSIMS)Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery10.1145/2484762.2484814(1-8)Online publication date: 22-Jul-2013
https://dl.acm.org/doi/10.1145/2484762.2484814
Simmerman SWang JOsborne JShook KHuang JGodsoe WSimons TStewart C(2012)Exploring similarities among many species distributionsProceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond10.1145/2335755.2335835(1-9)Online publication date: 16-Jul-2012
https://dl.acm.org/doi/10.1145/2335755.2335835

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