Download Cyberinfrastructure for Plant Biologists

Cyberinfrastructure 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.
What is still needed, however, is a way to
integrate the massive, disparate datasets,
algorithms, and tools, leveraging the
NSF’s billion-dollar investment to create a
comprehensive network of knowledge that
will advance humanity.
In 2008, the NSF initiated the “iPlant
Collaborative,” a $50 million, five-year
project to create the cyber- (or computer)
infrastructure needed to tackle “grand
challenge” questions in plant biology.
Developed by iPlant staff at Cold Spring Harbor Laboratory’s Dolan DNA Learning Center (DNALC), DNA Subway presents complex bioinformatics and visualization tools – predominantly open-source software – in an intuitive and appealing
is the first attempt at this scale to build a cyberinfrastructure that fills the gap between
the nation’s physical cyberinfrastructure — the supercomputers and networks — and the
kinds of computational analysis that plant scientists do everyday.”
iPlant will initially tackle two crucial problems in plant biology. The first, the “iPlant
Tree of Life” (iPToL), attempts to create a phylogenetic tree representing the diversity and
relationships between the world’s green plants. The second problem involves understanding
how a plant’s DNA combines with environmental conditions to give that plant its unique
traits.
“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 iPlant tree visualization application allows the user
to interactively explore extremely large phylogenetic
trees. This image is showing the National Center for
Biotechnology Information (NCBI) taxonomy tree,
containing approximately 260,000 species, zoomed in on the
Lamiales order.
The “Discovery Environment” (DE) is at the heart of iPlant. Modeled after Web 2.0
applications, like Wikipedia and Flickr, the DE allows community members to build content
in a democratic way, making connections between different types of data and integrating
information into a single user interface. The discovery environment incorporates existing
bioinformatics tools and runs them seamlessly on remote high-performance computing
resources. It also provides secure data management and editing environments for robust
production calculations.
Texas Advanced Computing Center | Feature Story
For more info, contact: Aaron Dubrow, Science and Technology Writer, [email protected]
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[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 genome
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
high-powered informatics tools that drive modern biology. Using
the subway metaphor, the application leads users through several
“stations” where they are able to annotate genes and perform genome
comparisons. The tool is currently available to all interested users.
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
Discovery Environment will provide access not only to tools built by the collaborative, but to
many community-contributed tools as well.
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]
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