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The Daily Wildcat

The Daily Wildcat

 

iPlant helps scientists tackle food issues

The UA is leading the creation of a cyber-infrastructure to help feed the world.

Among other things, iPlant Collaborative is a UA-led multi-college collective, which functions as a virtual marketplace to house information for plant biologists to solve larger global problems within their field.

Scientists can tackle issues, such as food insecurity or the problem of inbred plants, using a virtual desktop they can key into with a password and server log-in. These problems can also be addressed through community input and building the cyber-infrastructure foundation.

Before the virtual exchange, the spread of data was through shipping hard drives around the country, according to Stephen Goff, principal investigator and project director of the iPlant Collaborative. Now a click of the mouse lets people find out that same information in a fraction of the time.

A small project at the start, iPlant houses mostly scientists from Cold Spring Harbor Laboratory, computer scientists and code writers from the UA and the technology specialists at University of Texas, Austin, where the computers are housed.

Shannon Oliver, a senior studying microbiology and chemistry, started working at the BIO5 Institute, where iPlant is housed on campus, during her freshman year of college.

Daphne Gilman, her former boss and director of strategic alliances at BIO5, said Oliver has been flourishing while helping to write code for the new system.

Oliver has worked at six different labs during her undergraduate studies, but her one semester with iPlant has prepared her more than most other experiences for life outside of the university, she said.

“”Working at iPlant, even just one semester, has definitely prepared me for life outside of undergrad,”” Oliver said. “”It really stretched my ability to learn, and yet I had to learn fairly intricate computer science methods and programs, and it instilled in me the confidence that I can master something that complex.””

Oliver works in the discovery environment, an interface that facilitates scientific exploration and discovery through a common web interface.

“”There is absolutely no typical day in the office,”” Oliver said. “”We have to constantly collaborate and based it off of the interdisciplinary iPlant outlook. We are constantly in the environment, and we’re heading toward open source. … We want to be able for the community to contribute and with that we can drive innovation with a consistent integration.””

Goff said iPlant is looking for a continuation for the National Science Foundation’s grant to allow further collaboration between colleges and colleagues. The group was awarded $50 million in 2008 and has the potential to renew the grant for another five years for the same amount — and is using projects like Atmosphere to do it.

Atmosphere, the iPlant Collaborative’s cloud infrastructure service platform, allows applications created by computer scientists to be made accessible to biologists working on research to access programs that ease data collection and the findings of other biologists in the field.

Seung-jin Kim, infrastructure services integrator for iPlant’s Atmosphere, explained that the cloud system lets scientists “”not worry about how much space they’ll have.””

“”They don’t have to worry about if they need more space. We worry about that,”” Kim said. The UA’s role is to package each written application and make it user friendly for scientists.

Each type of scientist has a different language, Goff said, and learning to speak them all and have those with different vocabularies work together is a main mission of the iPlant team, as no other forum has the capacity to link this much information globally to plant scientists.

“”There are so many different needs for these tools and (facilitating) integration while still allowing scientists in the technical community to be free to put everything they need in there,”” Oliver said. “”Science is always changing and we’re constantly documenting so everyone has a good perspective on where our projects are going.””

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