The iPlant collaborative: cyberinfrastructure for plant biology

被引：298

作者：

Goff, Stephen A. ^{[1
]}

Vaughn, Matthew ^{[2
]}

McKay, Sheldon ^{[1
]}

Lyons, Eric ^{[1
]}

Stapleton, Ann E. ^{[3
,4
]}

Gessler, Damian ^{[1
]}

Matasci, Naim ^{[1
]}

Wang, Liya ^{[5
]}

Hanlon, Matthew ^{[2
]}

Lenards, Andrew ^{[1
]}

Muir, Andy ^{[1
]}

Merchant, Nirav ^{[1
]}

Lowry, Sonya ^{[1
]}

Mock, Stephen ^{[2
]}

Helmke, Matthew ^{[1
]}

Kubach, Adam ^{[2
]}

Narro, Martha ^{[1
]}

Hopkins, Nicole ^{[1
]}

Micklos, David ^{[6
]}

Hilgert, Uwe ^{[6
]}

Gonzales, Michael ^{[2
]}

Jordan, Chris ^{[2
]}

Skidmore, Edwin ^{[1
]}

Dooley, Rion ^{[2
]}

Cazes, John ^{[2
]}

McLay, Robert ^{[2
]}

Lu, Zhenyuan ^{[5
]}

Pasternak, Shiran ^{[5
]}

Koesterke, Lars ^{[2
]}

Piel, William H. ^{[7
]}

Grene, Ruth ^{[8
]}

Noutsos, Christos ^{[5
]}

Gendler, Karla ^{[2
]}

Feng, Xin ^{[5
,9
]}

Tang, Chunlao ^{[5
]}

Lent, Monica ^{[1
]}

Kim, Seung-Jin ^{[1
]}

Kvilekval, Kristian ^{[10
]}

Manjunath, B. S. ^{[10
,27
]}

Tannen, Val ^{[11
]}

Stamatakis, Alexandros ^{[12
]}

Sanderson, Michael ^{[13
]}

Welch, Stephen M. ^{[14
]}

Cranston, Karen A. ^{[15
]}

Soltis, Pamela ^{[16
]}

Soltis, Doug ^{[17
]}

O'Meara, Brian ^{[18
]}

Ane, Cecile ^{[19
,20
]}

Brutnell, Tom ^{[21
]}

Kleibenstein, Daniel J. ^{[22
]}

机构：

[1] Univ Arizona, Inst BIO5, Tucson, AZ 85721 USA

[2] Univ Texas Austin, Texas Adv Comp Ctr, Austin, TX 78712 USA

[3] Univ N Carolina, Dept Biol, Wilmington, NC 28401 USA

[4] Univ N Carolina, Dept Marine Sci, Wilmington, NC 28401 USA

[5] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA

[6] Cold Spring Harbor Lab, DNA Learning Ctr, Cold Spring Harbor, NY 11724 USA

[7] Yale Univ, Yale Peabody Museum, New Haven, CT USA

[8] Virginia Tech Univ, Dept Plant Pathol Physiol & Weed Sci, Blacksburg, VA USA

[9] Ontario Ctr Canc Res, Toronto, ON, Canada

[10] Univ Calif Santa Barbara, Ctr Bioimage Informat, Santa Barbara, CA 93106 USA

[11] Univ Penn, Dept Comp & Informat Sci, Philadelphia, PA 19104 USA

[12] Heidelberg Inst Theoret Studies, Sci Comp Grp, Heidelberg, Germany

[13] Univ Arizona, Dept Ecol & Evolutionary Biol, Tucson, AZ 85721 USA

[14] Kansas State Univ, Dept Agron, Manhattan, KS 66506 USA

[15] Natl Evolutionary Synth Ctr NESCent, Durham, NC USA

[16] Univ Florida, Florida Museum Nat Hist, Gainesville, FL 32611 USA

[17] Univ Florida, Dept Biol, Gainesville, FL USA

[18] Univ Tennessee, Dept Ecol & Evolutionary Biol, Knoxville, TN USA

[19] Univ Wisconsin, Dept Stat, Madison, WI 53706 USA

[20] Univ Wisconsin, Dept Bot, Madison, WI USA

[21] Cornell Univ, Boyce Thompson Inst Plant Res, Ithaca, NY 14853 USA

[22] Univ Calif Davis, Dept Plant Sci, Davis, CA 95616 USA

[23] USDA ARS, Arid Land Agr Res Ctr, Maricopa, AZ USA

[24] Univ Georgia, Dept Plant Biol, Athens, GA 30602 USA

[25] Yale Univ, Dept Ecol & Evolutionary Biol, New Haven, CT USA

[26] Univ Wisconsin, Dept Bot, Madison, WI USA

[27] Univ Calif Santa Barbara, Santa Barbara, CA 93106 USA

[28] Univ N Carolina, Dept Biol, Chapel Hill, NC USA

[29] Univ Arizona, Dept Comp Sci, Tucson, AZ 85721 USA

[30] Univ Arizona, Dept Elect & Comp Engn, Tucson, AZ 85721 USA

[31] Univ Arizona, Eller Sch Business, Tucson, AZ 85721 USA

[32] Cornell Univ, Dept Phys, Ithaca, NY 14853 USA

来源：

FRONTIERS IN PLANT SCIENCE | 2011年 / 2卷

基金：

美国国家科学基金会;

关键词：

cyberinfrastructure; bioinformatics; plant biology; computational biology; ARABIDOPSIS GENOME; COMPUTER-VISION; TAVERNA; BIOINFORMATICS; TOOL; PHYLOGENETICS; ARCHITECTURE; DISCOVERY; RESPONSES; SOFTWARE;

D O I：

10.3389/fpls.2011.00034

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

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 plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in 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 in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services.

引用

页数：16

共 75 条

[1] Convergence and correlations among leaf size and function in seed plants: A comparative test using independent contrasts
Ackerly, DD
Reich, PB
[J]. AMERICAN JOURNAL OF BOTANY, 1999, 86 (09) : 1272 - 1281
[2] Simultaneous Bayesian gene tree reconstruction and reconciliation analysis
Akerborg, Oerjan
Sennblad, Bengt
Arvestad, Lars
Lagergren, Jens
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (14) : 5714 - 5719
[3] Altintas I., 2004, 16 INT C SCI STAT DA
[4] [Anonymous], 6 DIV
[5] Bioinformatics in the orphan crops
Armstead, Ian
Huang, Lin
Ravagnani, Adriana
Robson, Paul
Ougham, Helen
[J]. BRIEFINGS IN BIOINFORMATICS, 2009, 10 (06) : 645 - 653
[6] Awano T, 2009, P NATL ACAD SCI USA, V106, P2794, DOI [10.1073/pnas.0812297106, 10.1073/pnas.0905845106]
[7] Getting to the root of plant biology: impact of the Arabidopsis genome sequence on root research
Benfey, Philip N.
Bennett, Malcolm
Schiefelbein, John
[J]. PLANT JOURNAL, 2010, 61 (06) : 992 - 1000
[8] Twenty-First Century Plant Biology: Impacts of the Arabidopsis Genome on Plant Biology and Agriculture
Buell, C. Robin
Last, Robert L.
[J]. PLANT PHYSIOLOGY, 2010, 154 (02) : 497 - 500
[9] From genome studies to agricultural biotechnology: closing the gap between basic plant science and applied agriculture
Cook, Douglas R.
Varshney, Rajeev K.
[J]. CURRENT OPINION IN PLANT BIOLOGY, 2010, 13 (02) : 115 - 118
[10] Deelman E., 2004, 2 EUR GRIDS C NIC

← 1 2 3 4 5 6 7 8 →