Navigation Links
BTI's Brutnell leads part of NSF Computational Plant Biology Research System
Date:3/23/2010

ITHACA, NY. Boyce Thompson Institute Associate Scientist Thomas Brutnell 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. 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 Brutnell 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. Brutnell's specific role is to help design a computational pipeline to process ultra high- throughput sequence datasets

"One of the great challenges in biology now is dealing with extremely large datasets, be it billions of bases of DNA sequence or millions of phenotypic measurements," said Brutnell, "We are working to make the processing and interrogation of these datasets easier."

"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," Brutnell 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 (alleles)," Brutnell said. "One of the questions is, can we breed for new traits based on a deeper understanding of the genetics in major crops? For example, we know that water will become more limiting in future agricultural settings. Can we find genes and pathways that help plants cope with water deficit? If so, we can then help plant breeders in identifying the most favorable alleles for their favorite crop"

Other leaders on the iPG2P team include Steve Welch, professor of agronomy at Kansas State University ; 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 University of Texas Advanced Computing Center, 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 individual biological problems but to develop the computational tools to work on the problem," Brutnell 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, Brutnell said, the University of Arizona and University of Texas are building extensive software systems to support the effort.


'/>"/>

Contact: Lorraine S. Johnson
lj25@cornell.edu
Boyce Thompson Institute for Plant Research
Source:Eurekalert

Related biology news :

1. Meth exposure in young adults leads to long-term behavioral consequences
2. Seattle Childrens Hospital leads $23.7 million NIH grant to study gene repair
3. UD leads $5.3-million research project on rice epigenetics
4. UD leads $5.3-million research project on rice epigenetics
5. Nature leads the way for the next generation of paints, cosmetics and holograms
6. Massive microRNA scan uncovers leads to treating muscle degeneration
7. Scripps Research discovery leads to broad potential applications in CovX-Pfizer deal
8. The construction of heart modelling leads path to new therapies
9. Eat less or exercise more? Either way leads to more youthful hearts
10. Virginia Tech plant scientist leads study on genomics of parasitic plants
11. Telecom research leads to solar cell breakthrough
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:3/2/2017)... , March 2, 2017 Australian stem cell ... (ASX: CYP), has signed an agreement with the Monash ... Monash Biomedicine Discovery Institute and Department of Pharmacology at ... a further preclinical study to support the use of ... asthma.  Asthma is a chronic, long ...
(Date:2/28/2017)... LOS ANGELES , Feb. 28, 2017   ... identity verification software globally, announces significant enhancements to new ... in May 2016. New products include mobile and desktop ... and DocX TM - a real time manual ... Acuant,s core idScan® technology provides the fastest and most ...
(Date:2/28/2017)... , Spanien, 27. Februar 2017  EyeLock LLC, ein ... wird seine erstklassige biometrische Lösung zur Iris-Erkennung ... mit X16 LTE auf dem Mobile World ... am Qualcomm-Stand in Halle 3, Stand 3E10, ... die Sicherheitsplattform Qualcomm Haven™ – eine Kombination ...
Breaking Biology News(10 mins):
(Date:3/23/2017)... 2017  GlobeImmune, Inc. today announced it has entered ... 12,835,490 shares of its common stock to NantCell, Inc., ... with the sale of its common stock, NantCell has ... to GlobeImmune 200,000 shares, an estimated $2.0 million in ... are pleased to enter into this strategic agreement with ...
(Date:3/23/2017)... , March 23, 2017 NetworkNewsWire ... ... death, putting significant strain on health care systems, in terms ... diagnoses rises, so too does the development of innovative and ... side effects. Among the many types of cancer treatments, a ...
(Date:3/23/2017)... La. (PRWEB) , ... March 23, 2017 , ... ... industrial monitoring solutions, today announced the hire of Dr. Sigmund “Sig” Floyd as ... customer applications, strategic partnerships and joint development activities. , “Dr. Floyd’s career has ...
(Date:3/22/2017)... MONICA, Calif. , March 22, 2017 /PRNewswire/ ... are proud to announce their extended partnership and ... will be headlined by the 21 st ... BIOMEDevice Boston, taking place May 3-4, 2017. ... Advanced Medical Technology Association (ADVAMED) President and CEO, ...
Breaking Biology Technology: