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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #284709
Title: The iPlant collaborative: cyberinfrastructure for plant biology

Author
item GOFF, STEPHEN - University Of Arizona
item VAUGHN, MATTHEW - University Of Texas
item MCKAY, SHELDON - University Of North Carolina
item LYONS, ERIC - University Of Arizona
item STAPLETON, ANN - University Of North Carolina
item GESSLER, DAMIAN - Cold Spring Harbor Laboratory
item MATASCI, NAIM - University Of Arizona
item WANG, LIYA - Virginia Tech
item HANLON, MATTHEW - Ontario Cancer Institute
item LENARDS, ANDREW - University Of California
item MUIR, ANDY - University Of Pennsylvania
item MERCHANT, NIRAV - University Of Arizona
item LOWRY, SONYA - University Of Arizona
item MOCK, STEPHEN - University Of Texas
item HELMKE, MATTHEW - University Of Arizona
item KUBACH, ADAM - University Of Texas
item NARRO, MARTHA - University Of Arizona
item HOPKINS, NICOLE - University Of Arizona
item MICKLOS, DAVID - University Of Wisconsin
item HILGERT, UWE - University Of Wisconsin
item GONZALES, MICHAEL - University Of Texas
item JORDAN, CHRIS - University Of Texas
item Skidmore, Edward
item DOOLEY, RION - University Of Texas
item CAZES, JOHN - University Of Texas
item MCLAY, ROBERT - University Of Texas
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item PASTERNAK, SHIRAN - Cold Spring Harbor Laboratory
item PIEL, WILLIAM - Yale University
item GRENE, RUTH - Virginia Tech
item NOUTSOS, CHRISTOS - Cold Spring Harbor Laboratory
item GENDLER, KARLA - University Of Texas
item FENG, XIN - Cold Spring Harbor Laboratory
item TANG, CHUNTAO - Cold Spring Harbor Laboratory
item LENT, MONICA - University Of Arizona
item KIM, SEUNG-JIN - University Of Arizona
item KVILEKVAL, KRISTIAN - University Of California
item MANJUNATH, B.S. - University Of California
item TANNEN, VAL - University Of California
item STAMATAKIS, ALEXANDROS - Heidelberg University
item SANDERSON, MICHAEL - University Of Arizona
item WELCH, STEPHEN - Kansas State University
item CRANSTON, KAREN - National Evolutionary Synthesis Center (NESCENT)
item SOLTIS, PAMELA - University Of Florida
item SOLTIS, DOUG - University Of Florida
item O'MEARA, BRIAN - University Of Tennessee
item ANN, CICILE - University Of Wisconsin
item BRUTNELL, TOM - Danforth Plant Science Center
item KLEIBENSTEIN, DANIEL - University Of California
item White, Jeffrey
item LEEBENS-MACK, JAMES - University Of Georgia
item DONOGHUE, MICHAEL - Yale University
item SPALDING, EDGAR - University Of Wisconsin
item VISION, TODD - University Of North Carolina
item MYERS, CHRISTOPHER - Cornell University
item LOWENTHAL, DAVID - University Of Arizona
item ENQUIST, BRIAN - University Of Arizona
item BOYLE, BRAD - University Of Arizona
item AKOGLU, ALI - University Of Arizona
item ANDREWS, GREG - University Of Arizona
item RAM, SUDHA - University Of Arizona
item Ware, Doreen
item STEIN, LINCOLN - Cold Spring Harbor Laboratory
item STANZIONE, DAN - University Of Texas

Submitted to: Frontiers in Plant Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/11/2011
Publication Date: 7/25/2011
Citation: Goff, S.A., Vaughn, M., Mckay, S., Lyons, E., Stapleton, A.E., Gessler, D., Matasci, N., Wang, L., Hanlon, M., Lenards, A., Muir, A., Merchant, N., Lowry, S., Mock, S., Helmke, M., Kubach, A., Narro, M., Hopkins, N., Micklos, D., Hilgert, U., Gonzales, M., Jordan, C., Skidmore, E.L., Dooley, R., Cazes, J., Mclay, R., Lu, Z., Pasternak, S., Piel, W.H., Grene, R., Noutsos, C., Gendler, K., Feng, X., Tang, C., Lent, M., Kim, S., Kvilekval, K., Manjunath, B., Tannen, V., Stamatakis, A., Sanderson, M., Welch, S.M., Cranston, K.A., Soltis, P., Soltis, D., O'Meara, B., Ann, C., Brutnell, T., Kleibenstein, D.J., White, J.W., Leebens-Mack, J., Donoghue, M.J., Spalding, E.P., Vision, T.J., Myers, C.R., Lowenthal, D., Enquist, B.J., Boyle, B., Akoglu, A., Andrews, G., Ram, S., Ware, D., Stein, L., Stanzione, D. 2011. The iPlant collaborative: cyberinfrastructure for plant biology. Frontiers in Plant Genetics and Genomics. DOI: 10.3389/fpls.2011.00034. 2:34.

Interpretive Summary: This manuscript provides a broad overview of the iPlant Collaborative to introduce scientists and educators to the purpose and resources of iPlant, and to highlight research projects currently in development that utilize iPlant. The value of iPlant is illustrated using a hypothetical example of a research scientist working to coordinate and execute a large multi-disciplinary, multi-institutional project to improve crop plant stress tolerance. The manuscript describes how researchers can exploit computational tools, data storage, and compute resources using iPlant’s Discovery Environment, detailing the cyberinfrastructure architecture, APIs, cloud computing service, and semantic web services. Active research and progress are described for the iPlant Grand Challenge Tree of Life and Genotype-to-Phenotype projects, as well as seed projects. The manuscript also describes iPlant’s Education Program, aimed at user training and bringing plant biology into the classroom.

Technical Abstract: 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 crossdisciplinary 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 opensource project with application programming interfaces that allow the community to extend the infrastructure to meet its needs.