Manhattan, Kansas, USA
March 3, 2010
Kansas State University professor of agronomy Steve Welch is helping lead a group of life scientists and computer researchers who are attempting to solve one of the "grand challenges" in the plant sciences.
The challenge is to predict how plants will grow and develop based on their particular genetic makeup and the various environments where they are found or planted. Solving this problem requires new computer software and computational capabilities, including powerful tools to allow scientists around the globe to collaborate on plant research.
The principles of iPlant, a nearly $50 million project funded by the National Science Foundation, include development of a cyberinfrastructure collaborative effort and also to train the next generation of scientists in computational thinking and to reinvent itself as the needs of the scientific community and technologies change, Welch said. The formal name of the five-year effort is the Plant Science Cyberinfrastructure Collaborative (PSCIC) program.
iPlant hosted workshops for researchers from the biological and computational sciences that yielded the "grand challenge" questions that iPlant would tackle, as well as the tools, strategies and approaches needed to find answers to the questions.
The particular iPlant team involving Welch is the Genotypes to Phenotypes in Complex Environments (iPG2P) committee, which will help researchers study the relationship between plant genotypes - the genetic makeup of particular plants - and how those genotypes interact and express themselves in various environments.
"One of the issues researchers face when working on such a project is simply understanding the vocabularies and viewpoints of other researchers in the many different fields that may have some bearing on what they are studying," said Welch, who is based in K-State´s Department of Agronomy. "We are working to make that collaboration easier."
"This is an exciting area. We have some of the best people in the world working on these projects," said Welch, who is a systems agronomist with K-State Research and Extension.
"In a world where the environment is undergoing rapid change, predicting altered plant responses is central to studies of plant adaptation, ecological genomics, crop improvement, plant development and more," Welch said. Crop improvement activities could involve impact areas from international agriculture to biofuels.
"In nature, individual plants, like people, will have their own particular set of genes," Welch said. "One of the questions is, what traits will a plant with specific genes develop given different environments? For example, we don´t know for sure how plants will respond to climate change. Will crops perform better or worse? Will the same be true of weeds? What about plants in natural ecosystems? And how do the answers to these questions vary from place to place?"
Other K-State faculty working on the project are Sanjoy Das, associate professor in electrical and computer engineering and Doina Caragea, assistant professor of computer science.
Other leaders on the iPG2P team include Tom Brutnell, molecular geneticist at the Boyce Thompson Institute; Doreen Ware, computational biologist with the U.S. Department of Agriculture´s Agricultural Research Service; Dan Kliebenstein, plant physiologist at University of California, Davis; Ruth Grene, plant physiologist at Virginia Tech; Chris Myers, computational biologist at Cornell University; Steve Goff, iPlant project director at the University of Arizona; Dan Stanzione, deputy director of the Texas Advanced Computing Center at The University of Texas at Austin; and Matt Vaughn, specialist in computational genomics at Cold Spring Harbor Laboratory, New York.
"Plants are good systems to work in, but genotype to phenotype issues go across all biology. Our task is not to solve the problem but to develop computer support to work on the problem," Welch said. "When finished, iPlant computer systems will be able to handle huge amounts of data and able to create computer displays in easy-to-understand forms."
In addition to the iPlant working groups, Welch said, the University of Arizona and University of Texas are building extensive software systems to support the effort.
More information about iPlant is available on the Web at http://www.iplantcollaborative.org/.
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