The University of Arizona Alumnus / Spring 2008
iPlant Collaborative to Tackle the World's Most Complex Problems
"Our goal is to organize the world’s information on plant sciences and to provide sophisticated computational and analytical tools to ‘ash things up,’ as they say in the Web 2.0 world." — Richard Jorgensen professor of plant sciences
by John Brown
Photos by John Sartin
“New wheat crisis plagues world food supply.”
“Could we really run out of food?”
Recent news headlines point to significant shifts in the global food-supply chain that are causing a ripple effect from your pocketbook all the way to the Amazon.
And the stakes are much higher than pricey chicken noodle soup. Recent evidence strongly suggests that dramatic increases in biofuel production — originally seen as an answer to global warming — actually may be doing more harm than good.
As prices for wheat, corn, and soybeans tripled in recent years, huge swaths of the Amazon forest have been cleared for new crop production, rapidly depleting the planet’s most important location for storing carbon.
High demand for biofuel pits feeding mouths versus cars. The amount of corn needed to fill an ethanol-fueled SUV can feed one person for a year. And with the world’s population expected to top 10 billion people by 2050, the choices we make about how to use finite natural resources only become more difficult.
As more natural habitat is cleared for housing and food production, what are the effects on the environment? How do we manage water consumption? How do we develop more productive crops that also are more disease and drought resistant? How will huge shifts in human migration patterns affect climate change?
These are just a sampling of the questions facing the global society. To get to the answers, a $50-million National Science Foundation grant is funding the iPlant Collaborative, a UA-led effort to unite the world’s leading scientists in solving plant biology’s biggest mysteries.
The UA’s BIO5 Institute will serve as the physical center for developing a Web-based virtual computing space that uses MySpace-like social networking tools to foster collaboration among plant biology researchers and computer engineering experts.
This first-of-its-kind global community of researchers promises to provide transformative discoveries — from minute processes of individual plant cells to patterns of entire ecosystems — that are fundamental to understanding the long-term sustainability of life on our planet.
“We need to understand how the biology of plants works, how plants interact with each other and relate to other organisms, how they participate in ecosystem function, and ultimately, how they are going to respond to changes in climate and changes in ecosystems that are caused by climate,” says Richard Jorgensen, Ph.D., professor of plant sciences at the UA.
In April, nearly 200 plant scientists and computer and information experts from
around the world met at Cold Spring Laboratory in New York — while hundreds more participated over the Internet — to discuss the formation of the grand challenge questions that will direct the scope of the project.
An independent board of directors, a collection of leading scientists not directly involved in the research, will determine the grand challenge questions based on submissions from scientists worldwide.
“A key concept is that this is a collaborative of, for, and by the community,” says Vicki Chandler, Ph.D., director of the BIO5 Institute. “Those of us who are principal investigators see ourselves as facilitators of accomplishing this goal. This is a very different kind of grant project than what is typically funded by the federal agencies requiring specific research goals spelled out in detail ahead of time.”
The iPlant project will not generate new data. Instead, it will facilitate the sharing of existing data and encourage new research teams to form and conduct studies where information gaps exist.
“It’s kind of a sophisticated version of Google,” Jorgensen says. “Our goal is to organize the world’s information on plant sciences and to provide sophisticated computational and analytical tools to ‘mash things up,’ as they say in the Web 2.0 world.”
iPlant Collaborative to Engage K-12 Students
by John Brown
The iPlant Collaborative's Web-based social networking and computational tools will allow K-12 students to actively participate in virtual research, alongside the world's top scientists.
"Not only do we have the opportunity to revolutionize how research is done, we also have the opportunity to revolutionize how education is done,?says BIO5 Director Vicki Chandler, who is the management lead for the project’s Education, Outreach, and Training (EOT) program.
The EOT plans to develop age-appropriate Internet modules that teachers can incorporate into classroom curriculum. In addition to teacher training, there will be six-week research projects for high-school students, with middle-and elementary-school-level components being developed.
"The goal is to produce a new generation of students who understand not only how to use computers, but also how to apply computational processes to important biological questions,?she says.
The dynamic, interactive nature of the iPlant Web portal will provide students real-time access to data as it's generated by the researchers, allowing for a first-of-its-kind educational experience.
"Students will be able to come up with hypotheses, test them, and provide immediate feedback to the scientists," Chandler says, adding that anyone connected to the Internet can play."People all over the world will be participating in this. It's really exciting."
The Dolan DNA Learning Center (DNALC), renowned for its Web-based learning tools for genomics and bioinformatics, is developing multimedia outreach and teaching modules in partnership with teachers. Video, podcasts, and narrated animations will explain the conceptual background for the iPlant project and the process for teachers to involve their students in the research.
The EOT team includes Dave Micklos, executive director of the DNALC at Cold Spring Harbor Laboratory, as well as experts from the UA, other universities, and an external advisory committee with representatives from various educational backgrounds. Workshops planned around the country will train educators on how to use the iPlant education tools.
iPlant's Cyberinfrastructure: Part Facebook, Part Supercomputer
by John Brown
The backbone of the iPlant Collaborative is the cyberinfrastructure that will facilitate the joining of ideas and people. This community of scientists will use Web-based applications to combine and analyze datasets in new, more meaningful ways.
In April 2008, nearly 200 plant, computer, and information scientists from around the world met at Cold Spring Laboratory in New York to discuss the grand challenge problems in plant biology and the computing capabilities the project requires to tackle them.
The physical "brains" of the operation ?computer servers, data warehouses, and high-speed networking hardware for iPlant ?are being developed under the supervision of Gregory Andrews, Ph.D, UA professor and interim head of the Department of Computer Science.
The software — a hybrid of existing and specially designed applications — will support "discovery environments' that allow biologists to seamlessly access and link previous silos of data and analytical techniques together for advanced modeling and analyses," says Sudha Ram, Ph.D, McClelland professor of management information systems at the UA.
The goal is to maximize the strengths of computer and human thinking power to foster a multidisciplinary environment for separating grand challenge questions into smaller, manageable subproblems that can be examined individually.
"Computational thinking allows us find a solution to each subproblem using simple methods — some of which you may already know or have seen before — and then put it all together for an overall solution that provides new insights," Ram says. " It's all about seeing patterns of similarity and, over time, learning to automatically apply these patterns to solve problems."
The collaboration and social networking aspects of the iPlant portal will allow scientists with like interests to team up, solve subproblems, and share findings.
"It's match.com for scientists — each new finding or discovery will be visible to the online community of researchers,"Ram says. "The more findings you share, the more discoveries you can make."
The Web portal's open-source development philosophy will allow "the user community to take ownership of the project," Ram says. "We are going to produce software products in response to the community's needs, then document how they evolve over time and how they work in the real world."
Researchers hope iPlant's capabilities will evolve to include Google Earth-like qualities. For instance, a researcher might zoom in to analyze the oxygen produced by individual plants, then zoom out to analyze how large-scale changes in the number of those plants present in an ecosystem could affect air quality or climate change.
Ram says business executives familiar with the project are interested in the innovations it will inspire for the private sector.
"What we're proposing is a completely new paradigm for collaborative research among a diverse community," Ram says. "It also offers a whole new business model for how companies should approach the development of information technology solutions."
BIO5 Institute
The foresight of the Arizona legislature, the Arizona Board of Regents, and private donors in establishing the BIO5 Institute and constructing its new research building is paying off. BIO5¡¯s administrative infrastructure and its collaborative research mission are factors that contributed to iPlant¡¯s success in competing for this award.
One source of BIO5¡¯s state funding is the Technology and Research Initiative Fund (TRIF), a special investment in higher education supported by a voter-approved tax in 2001. UA alumnus Thomas W. Keating donated $10 million toward construction of BIO5¡¯s new 172,000-square-foot research building and House Bill 2529 covered the balance.
BIO5 stimulates interaction among scientists from five disciplines ¨C agriculture, medicine, pharmacy, basic science, and engineering ¨C to solve complex problems. BIO5 faculty discoveries in areas such as disease prevention and food production have spurred many innovations and the formation of 11 companies over the years.
BIO5 Institute: By the Numbers
Square feet: 177,000
Building cost: $51.1 million, or about $289 per sq. ft.
350-plus researchers, 40 percent of which are students
What they said...
¡°The $50-million NSF grant is proof that our investment in higher education is paying off. Arizona¡¯s future lies in innovation in areas like the biosciences.¡±
¡ª Arizona Governor Janet Napolitano
¡°This is the sort of big return on investment that the UA has promised the state of Arizona since the BIO5 Institute was opened and housed with critical state investments.¡± ¡ª UA President Robert N. Shelton
¡°This remarkable grant recognizes the great work being done every day by the researchers and students of The University of Arizona ¡ The UA has emerged as a leader in bioscience research and education.¡± ¡ª Congressman Raul Grijalva
¡°The learning activities that will evolve from the iPlant collaborative will bring the challenges of real-world problem-solving and discovery to the classroom for both students and teachers.¡±
¡ª President and CEO of Science Foundation Arizona William C. Harris
Vicki Chandler, Ph.D., Director, BIO5 Institute
Carl E. and Patricia Weiler Endowed Chair in Excellence
BIO5 Institute Director Vicki Chandler has participated in pioneering biology research all over the world. So when she says that working on the iPlant Collaborative is the ¡°most stimulating activity I¡¯ve been involved in,¡± you know this project is serious.
¡°The team at the UA, as well as Cold Spring Harbor, ASU, and the other project partners, is just a spectacular group of people to work with,¡± Chandler says. ¡°It¡¯s very challenging and a lot of work, but it¡¯s been a fun ride.¡±
A fun ride characterizes her entire career. Chandler is internationally recognized in the field of regulation of gene expression in plants and animals. Her research has advanced scientists¡¯ understanding of plant genetics and human disease.
Since taking the helm of BIO5 in 2004, Chandler has positioned the institute to fuel statewide efforts to grow the bioscience industry in Arizona. In 2007, she was named the Ed Denison Business Leader of the Year at the Arizona Governor¡¯s Celebration of Innovation.
Chandler joined the UA faculty in 1997. A Regents¡¯ Professor in the Departments of Plant Sciences and Molecular and Cellular Biology, she occupies the Weiler Endowed Chair for Excellence in Agriculture and Life Sciences.
The about $40,000 in unrestricted annual funding the chair provides has been invaluable to her research.
Federal grants typically contain very specific benchmarks and narrow research scopes, making tangential investigations tough to pursue.
¡°If you discover something that might lead you in a new direction, you really don¡¯t have the flexibility of doing that,¡± she says. ¡°And it¡¯s often difficult to get funding for a research project if you don¡¯t have preliminary data.¡±
Chair funds support pilot projects that allow team members to test intriguing hypotheses. ¡°We often can use the preliminary data to write a major funding proposal to launch the project in a big way,¡± she says. ¡°It¡¯s that kind of flexibility that¡¯s very attractive and useful.¡±
Chandler earned a bachelor¡¯s degree in biochemistry at the University of California, Berkeley, and a doctorate in biochemistry from the University of California, San Francisco. She was a National Science Foundation Plant Postdoctoral Fellow in the Department of Biological Sciences at Stanford University.
¡ª John Brown
The iPlant Collaborative — www.iplantcollaborative.org
Research Institutions The University of Arizona |
Rebecca W. Doerge, Ph.D.Professor, Departments of Agronomy and Statistics,
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UA Participants The BIO5 Institute |
Nirav Merchant, Ph.D.Director, Biotechnology Computing Facility at the Arizona Research Laboratories (ARL), The University of ArizonaMerchant is the principal systems architect for multi-institutional research projects at the ARL division of biotechnology. He oversees the campus Biotechnology Computing Facility, which provides core infrastructure for research, education, and training support in life sciences informatics. |
iPlant Board of Directors Robert Last, Ph.D., of Michigan State University, will chair the project’s board of directors, a collection of leading scientists not directly involved in the research who will provide oversight. Last’s studies include how plants make molecules that are nutritionally important to humans and provide protection against environmental stress. |
Sudha Ram, Ph.D.McClelland Professor of Management Information Systems,
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Principal Leadership Team Richard Jorgensen, Ph.D.Professor of Plant Sciences
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Daniel Stanzione, Ph.D.Founding Director, Fulton High Performance Computing Initiative (HPCI) at Arizona State UniversityThe HPCI is the central hub for research computing at ASU and engages (with almost 100 faculty members) across more than 20 disciplines dealing with large-scale computational models and large volumes of data. Stanzione’s research includes a long-standing interest in the development of problem-solving environments to support scientists in using high-end computing resources. |
Gregory Andrews, Ph.D.Professor and Interim Head, Department of Computer Science The University of ArizonaGreg Andrews’ research interests include all aspects of parallel and distributed computing, from hardware architectures to software applications. He is leading the effort of building the hardware platform that will support iPlant’s Web community and discovery environments for data analysis. |
Ann E. Stapleton, Ph.D.Associate Professor, Department of Biology and Marine Biology University of North Carolina at WilmingtonAnn E. Stapleton is internationally recognized as an expert in plant responses to ultraviolet radiation. Her research interests include analysis of the perception and response of plants to abiotic stress. Stapleton also has several interdisciplinary collaborations, ranging from bioinformatics software development to development of Bayesian statistical models. |
Vicki Chandler, Ph.D.Director, BIO5 Institute, Professor of Plant Sciences
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Lincoln Stein, MD, Ph.D.Cold Spring Harbor LaboratoryLincoln Stein takes a proactive approach to the current information explosion in genomics. His lab develops databases, data analysis tools, and user interfaces to organize, manage, and visualize the billions of bits of genomic data generated by the Human Genome Project and by new technologies for analyzing genetic data such as DNA microarrays and high-throughput genotyping. Lincoln is the co-leader of the team developing the software applications that will support discovery environments for iPlant researchers. |
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