for Plant Biologists The iPlant Collaborative releases new web-based tools to help plant scientists integrate Plants are the source of our food supply and breathable air. They are vital for carbon capture, bio-fuel production, and new pharmaceuticals. In fact, so much of society’s current and future health and well-being are tied to plant science that over the past decade, the National Science Foundation (NSF) has supported projects in the field with more than a billion dollars in funding.

Developed by iPlant staff at Cold Spring Harbor Laboratory’s Dolan DNA Learning Center (DNALC), DNA Subway pres- What is still needed, however, is a way to ents complex and visualization tools – predominantly open-source software – in an intuitive and appealing integrate the massive, disparate datasets, algorithms, and tools, leveraging the is the first attempt at this scale to build a cyberinfrastructure that fills the gap between NSF’s billion-dollar investment to create a the nation’s physical cyberinfrastructure — the supercomputers and networks — and the comprehensive network of knowledge that kinds of computational analysis that plant scientists do everyday.” will advance humanity. iPlant will initially tackle two crucial problems in plant biology. The first, the “iPlant In 2008, the NSF initiated the “iPlant Tree of Life” (iPToL), attempts to create a phylogenetic tree representing the diversity and Collaborative,” a $50 million, five-year relationships between the world’s green plants. The second problem involves understanding project to create the cyber- (or computer) how a plant’s DNA combines with environmental conditions to give that plant its unique infrastructure needed to tackle “grand traits. challenge” questions in plant biology. “Why do some plants flower faster? What is the relationship between their DNA and how “We are facing a lot of challenges in food they behave?” Stanzione asked. “We want to take genetic information about plants and production and food security going forward understand how that maps to expressed characteristics.” and iPlant puts together the computational framework by which researchers will This March, iPlant announced the beta release of the first set of computational environments address these grand challenges,” said and software frameworks designed to help plant scientists make discoveries faster. The Dan Stanzione, co-director of the iPlant “Discovery Environment,” “DNA subway” prototype, and “Tree of Life” visualization Collaborative and deputy director of the tool provide the first glimpse into the types of infrastructure that iPlant will integrate and Texas Advanced Computing Center. “iPlant distribute.

Web-based and easy-to-use, these tools allow scientists to perform remote computation and analysis on supercomputers. By drawing on the resources and expertise of the nation’s supercomputing centers and their staff, plant scientists, in collaboration with computer scientists and information scientists, will move closer to addressing critical questions in plant biology.

The “Discovery Environment” (DE) is at the heart of iPlant. Modeled after Web 2.0 applications, like and Flickr, the DE allows community members to build content The iPlant tree visualization application allows the user in a democratic way, making connections between different types of data and integrating to interactively explore extremely large phylogenetic information into a single user interface. The discovery environment incorporates existing trees. This image is showing the National Center for Biotechnology Information (NCBI) taxonomy tree, bioinformatics tools and runs them seamlessly on remote high-performance computing containing approximately 260,000 species, zoomed in on the resources. It also provides secure data management and editing environments for robust Lamiales order. production calculations.

Texas Advanced Computing Center | Feature Story For more info, contact: Aaron Dubrow, Science and Technology Writer, [email protected] Page 1 of 2 [A beta version of the Discovery Environment provides a working demonstration of its architecture and features, including the ability to analyze tree and trait data. iPlant is accepting account requests for access to this release, which is intended to give the community a sense of the direction that development is taking.]

The Tree of Life visualization tool is just one of many applications that will ultimately be built into the Discovery Environments, some by the iPlant Collaborative team, but many more from the community. The TreeVis tool revolutionizes the way phylogenetic trees are represented by introducing interactivity, scalability, and new ways of visualizing the connections between plants. The tool allows researchers to explore the relationships between distant or closely related species, to trace the historical sequence of reorganizations, or to examine patterns of adaptation in terms of geographic variance, climatic change, or co-evolution.

The “DNA Subway,” which complements the Discovery Environments, is a learning environment where students, educators, and researchers can access the large-scale datasets and The Discovery Environment provides a modern, common web interface and platform to expose the computing, data, and application resources made available to the community. The high-powered informatics tools that drive modern biology. Using Discovery Environment will provide access not only to tools built by the collaborative, but to the subway metaphor, the application leads users through several many community-contributed tools as well. “stations” where they are able to annotate genes and perform genome comparisons. The tool is currently available to all interested users.

Together, these new frameworks leverage existing and emerging applications, as well as the network of computational resources, to help scientists analyze, visualize, and make meaningful discoveries about plants and their DNA, far faster than ever before.

Said Stanzione, “By removing the grunt work of science — the need to manually convert data sets or to make a tool fit the data set that you’re working on — this project enables us to get to solutions more quickly, speeding scientific progress.”

Published June 9, 2010

Texas Advanced Computing Center | Feature Story For more info, contact: Aaron Dubrow, Science and Technology Writer, [email protected] Page 2 of 2