Backgrounder: A Collaborative Endeavor
The iPlant Collaborative will bring together researchers in every plant biology discipline—from those working at the microscopic level, such as molecular biologists, cellular biologists and geneticists, to those working on the ecosystem and planetary level—in partnership with computer scientists and engineers, information scientists, mathematicians and social scientists, in order to facilitate communication and collaboration across all of these disciplines and provide tools so that these specialists can work together more effectively than they have in the past.
Collaboration is central to iPlant because it’s central to how science now done; scientists can no longer work in isolation from one another. Every discipline relies on the disciplines around it, and the boundaries between disciplines are no longer sharply defined. A geneticist might need to work closely with an ecologist, for instance, to understand the underlying causes of changes in a species’ genetic code and their consequences for the species’ adaptation to the environment. A team of plant biologists gathering data about a species’ genome and the environmental changes that affect that species might need to work closely with computer and information scientists to organize, analyze and interpret those data.
“Computer and information scientists are trying to understand the problems that plant biologists face and then develop new innovative solutions to meet their needs,” explains Sudha Ram, PhD, McClelland professor of management information systems. “We’re devising these solutions together to advance all our fields. They’re solutions none of us can come up with on our own.” The resulting knowledge and tools will not only help solve biology’s grand challenge questions; they will also advance the cutting edge of all of these fields.
Social scientists will work with iPlant researchers to design social networking software for iPlant’s cyberinfrastructure that will facilitate communication among iPlant users in much the way Facebook facilitates communication among students who share a school or employees who share a workplace. iPlant’s social networking tools will make extensive use of web 2.0 applications such as wikis, blogs, online forums, chat rooms and messaging software, as well as more sophisticated analytical tools, in order to create “discovery environments” that will be custom-designed for the solution of plant biology’s “grand challenge” where collaboration and innovation can occur, and where researchers can access new tools to take on new questions they couldn’t address before. For instance, understanding the ability of wild plants to adapt to changes in soil moisture associated with climate change will require researchers to bring together genetic data and plant stress and growth data on natural populations and to map this information onto local climatological, weather, soil moisture, nutrient and mineral data.
The entire research community will have access to all of iPlant’s tools. So will students, teachers and the general public. “To solve plant biology’s grand challenges we need to work more collaboratively than we ever have before,” explains UA plant biologist Richard Jorgensen, PhD. “Operating independently—trying to be an island—is no longer tenable or sustainable.”
Importantly, the iPlant Collaborative is “by, for and of the community”. This means that the scientific community will choose the grand challenges in plant biology for which iPlant scientists will develop discovery environments. These decisions will be made through a community-representative board of directors that is being assembled by Robert Last, a plant biologist at Michigan State University, who will serve on the behalf of the community as chair of the board of directors.
Backgrounder: Tackling Plant Biology’s Grand Challenges
The iPlant Collaborative will empower the answering of plant biology’s grand challenge questions—those questions that are as fundamental to the plant sciences as understanding the speed of light or the nature of nuclear reactions once was to physics.
The first step to answering grand challenge questions is determining exactly which questions merit grand challenge status. Grand challenge questions must be potentially answerable; they also must have practical applications and societal implications. The plant biology, computer science, information science and mathematics communities will work collaboratively to set further grand challenge criteria, both at an iPlant kickoff meeting and through a series of follow-up workshops.
“We are the facilitators,” explains UA plant biologist Richard Jorgensen, PhD. “We’re bringing the research community together to create the iPlant Collaborative to facilitate their choices/decisions about which are the most important problems in plant biology today.” Categories of grand challenge questions that the community might choose to focus on include, but are not limited to, questions such as how plants grow from a single cell into complex, multi-cellular organisms; how and to what extent plants can adapt to environmental changes; how plants have evolved in the past and their potential to evolve in the future; and how plants live together with other organisms in ecosystems.
Once the grand challenge criteria have been set through community input, self-forming teams from around the country and around the world will propose specific grand challenge questions for iPlant to tackle. Anyone can propose a grand challenge question; the iPlant Collaborative’s external board of directors will select two to four initial questions to focus on in the first year, from as broad a spectrum of plant biology disciplines and subdisciplines as possible. iPlant’s team of plant biologists, computer scientists, information scientists, mathematicians and social scientists will then set about building a “Discovery Environment” (a cyberinfrastructure) to answer those questions in partnership with the community’s grand challenge teams.
Future rounds of grand challenge questions will make use of and build upon the same cyberinfrastructure. “The tools we build will be applicable to all kinds of data sets and all kinds of grand challenge problems,” Jorgensen says. “Ultimately, they will serve as a model for other fields as well.”
Backgrounder: Creating a Cyberinfrastructure
iPlant’s cyberinfrastructure is essentially an electronic meeting and analysis place, one where researchers from all disciplines can gather, analyze and share data; ask questions and search for answers; and talk with one another about what they find and what those findings mean. iPlant’s evolving team of plant biologists, computer and information scientists, mathematicians and social scientists will work collaboratively with other community scientists and experts brought in as the project demands to design the hardware and software that will run this virtual space.
“At its most basic, a cyberinfrastructure is a large collection of computing facilities—fast processors to run experiments, large amounts of storage for data repositories, advanced graphics facilities for visualizing results, and high-speed networks to make the collection accessible from remote locations. But to make such a facility truly usable, there has to be a software interface that makes the facilities easy to use and that supports experimentation and discovery,” says Gregory Andrews, PhD, UA professor and interim head, Department of Computer Science.
The cyberinfrastructure—and the researchers who use it—will rely on a method of problem-solving known as computational thinking. “Computational thinking basically asks, ‘What are the things that human brains don’t do very well that computers do well?’ and ‘What are the things that computers don’t do very well that human brains do well?’” explains UA plant sciences professor Richard Jorgensen, PhD.
What computers do well, among other things, is gather large amounts of data and perform calculations on those data. Letting iPlant’s cyberinfrastructure handle these tasks will free up researchers to focus on more creative work, such as interpreting the calculations and seeking creative, big-picture answers to plant biology’s grand challenge questions. Yet while more and more different types of plant biology data are available, researchers do not yet have all the computational tools to bring these disparate data sets together, analyze them efficiently, formulate new hypotheses, and empower the answering of plant biology’s grand challenge questions.
“Computational thinking is a way to look at a problem that you have never encountered before, figure out how to break it into bite-sized chunks, find a solution to each chunk using simple methods you may already know or have seen before, and then put it all together so you have an overall solution that works effectively and provides new insights,” says Sudha Ram, PhD, McClelland Professor of Management Information Systems. “It’s all about seeing patterns of similarity and, over time, learning to automatically apply these patterns to solve problems.”
Computational thinking can be applied to everything from daily life tasks such as finding the fastest way to the nearest grocery or choosing the best stocks to build a retirement portfolio to complex scientific problems such as devising cost-effective ways to clean up the earth’s atmosphere. It requires a combination of many skills, including logical thinking, creativity and innovation, dealing with uncertainty, teamwork, and interdisciplinary collaboration. Computational thinking also requires a person to be open minded enough to look at problems and problem-solving techniques from outside of their own areas of expertise to see if those techniques can be adapted to the current problem.
As the amount of information housed by iPlant’s cyberinfrastructure grows, its cyberinfrastructure will become a map of the terrain of plant biology, in much the way that Google Earth is as a map of our planet. Like users of Google Earth, users of iPlant may one day be able to “zoom” in and out among various levels of detail, viewing small details in the context of larger ones and large details in the context of smaller ones. 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 ecosystems could affect air quality or climate change.
iPlant’s cyberinfrastructure also will contain a strong social networking research component designed to facilitate communication and collaboration across disciplines, and it will contain learning tools for teachers and K–12, undergraduate and graduate students.
Backgrounder: Reaching Out to Teachers, Faculty, Students of All Ages and Beyond
Educational outreach is a central part of the iPlant Collaborative. The cyberinfrastructure designed to serve researchers seeking answers to grand challenge questions will also be adapted to serve K–12 students and teachers and faculty and students at community colleges, four year colleges, and major research universities. “iPlant offers an unprecedented opportunity to involve teachers and students in leading edge biology,” says BIO5 director Vicki Chandler, PhD.
Students and teachers at all levels will have access to the same resources that iPlant researchers themselves do. They’ll also have access to educational tools designed especially for them, such as modules focused on plant biology topics and online games designed to encourage learning. A major partner for the development of online tools is the Dolan DNA Learning Center at Cold Spring Harbor Laboratory, one of the world’s largest providers of multimedia learning materials for biology education and the maintainer of 11 Internet sites that received seven million visitors in 2006. iPlant will also offer teachers internships where they can help design teaching tools for their classrooms, and it will offer students the chance to do research side by side with iPlant graduate students and postdocs. National Science Foundation funding is being used to implement these programs nationally, while BIO5 and Science Foundation Arizona funds will be used to implement within Arizona.
All of the grand challenge questions iPlant takes on will, ultimately, have educational components. “Education will be thoroughly integrated into everything we do,” Chandler says. “iPlant is an excellent way to promote inquiry-based learning and get kids excited about science by showing them that they can do science themselves in very hands-on ways.”
The larger community is also being kept in mind as iPlant develops its cyberinfrastructure and chooses its grand challenge questions. Every accepted grand challenge proposal will have both practical applications and wider societal implications.
Educating the next generation of researchers has societal impacts of its own. “Economic reports show that the quality of life our country enjoys today exists because of the technology we’ve developed over the last 50 years,” Chandler explains, “but the United States is losing its edge in innovation and technological ability. We have to engage more young people in studying science. Our world depends on it.”
Richard Jorgensen, PhD
Professor of Plant Sciences, College of Agriculture and Life Sciences, The University of Arizona (UA)
Plant geneticist Richard Jorgensen is a recognized international leader in the fields of epigenetics and functional genomics. His research accomplishments include the discovery of a gene-silencing phenomenon in plants called cosuppression, later shown to be the same as RNA interference in animals and possibly to have major implications for the treatment of diseases such as cancer, hepatitis and AIDS.
Jorgensen was awarded the Martin Gibbs Medal in 2007 for his groundbreaking work in cosuppression and RNA interference by the American Society of Plant Biologists (ASPB). He was elected an Inaugural Fellow of the ASPB in 2007 and a Fellow of the American Association for the Advancement of Sciences in 2005. He has published in numerous scientific publications and is regularly invited to present his research findings at universities, research institutions and scientific conferences around the country and around the world.
Jorgensen has served as editor in chief of The Plant Cell, the leading research journal in plant biology, since 2003. He is series editor for the book series Plant Genetics and Genomics: Crops and Models. He has also organized several important scientific conferences, including ASPB’s Plant Genetics 2003 and Plant Genetics 2005, as well as the Gordon Research Conference on Plant Cell Genetics and Development in 1995.
Prior to his academic positions at the UA and previously UC Davis, he spent seven years working in the agricultural biotechnology industry in California.
Gregory Andrews, PhD
Professor and Interim Head, Department of Computer Science, The University of Arizona (UA)
Greg Andrews’ research interests include all aspects of parallel and distributed computing, from hardware architectures to software applications.
Andrews received a bachelor’s of science degree in Mathematics from Stanford University in 1969 and a doctorate in Computer Science from the University of Washington in 1974. From 1974 to 1979 he was an Assistant Professor at Cornell University. He has been at UA since 1979, where he is a Professor of Computer Science. He was Head of the Department from 1986 to 1993 and currently serves as Interim Head. From 2003 to 2005 he was a Division Director in the Computer and Information Science and Engineering Directorate of the National Science Foundation, first for Experimental and Integrative Activities, and then as the founding director of Computer and Network Systems.
He received a distinguished teaching award in 1986 and a career distinguished teaching award in 2002, both from the UA College of Science. In 1998, Andrews was named a Fellow of the Association for Computing Machinery.
From 1988 to 1992, Andrews served on two advisory committees for the computing directorate of the National Science Foundation (NSF). He served on the Board of Directors of the Computing Research Association from 1991 to 1998. Since 2006, he has been on the Council of the Computing Community Consortium, a national NSF-funded effort to provide scientific leadership and vision for computing research and future large-scale computing projects.
He has written dozens of journal and conference papers and is the author of three books: Concurrent Programming: Principles and Practice (Benjamin/Cummings, 1991), The SR Programming Language: Concurrency in Practice (Benjamin/Cummings, 1993, with Ron Olsson), and Foundations of Multithreaded, Parallel, and Distributed Programming (Addison Wesley, 2000).
Vicki Chandler, PhD
Director, BIO5 Institute, The University of Arizona (UA)
Since taking the helm of BIO5 in 2004, Vicki Chandler has positioned the institute to fuel statewide efforts to grow the bioscience industry in Arizona. Under her leadership, BIO5 focuses on fostering cutting-edge interdisciplinary research, driving innovations to market and improving science education to ensure a capable workforce.
Chandler serves on the Flinn Foundation’s Arizona Bioscience Roadmap Steering Committee and the National Advisory Board for C-Path, and is an appointed Commissioner for the State of Arizona Department of Commerce and Economic Development.
A Regents’ Professor in the UA departments of Plant Sciences and Molecular and Cellular Biology, she holds the Weiler Endowed Chair for Excellence in Agriculture and Life Sciences. In the early stages of her career, she received the Presidential Young Investigator and Searle Scholar awards. In 2002, Chandler was elected to the National Academy of Sciences. She was also elected a Fellow of the American Association for the Advancement of Science, and she is a nationally and internationally recognized leader in the epigenetic regulation of gene expression and gene silencing in plants and animals.
Her research results have significant implications, not only for plant genetics, but also for understanding human disease, as evidenced by the receipt of a NIH Director’s Pioneer Award in 2005—a first for an Arizona scientist. Chandler is frequently asked to present her latest research findings in national and international venues, and she has written more than 80 scientific papers for top quality journals in her field.
Chandler serves on scientific advisory boards for four biotechnology companies, Arcadia, Edenspace, High Throughput Genomics, and the Boyce Thompson Institute for Plant Research. She is an elected member of the governing council of the National Academies of Science and has also served in elected leadership roles in the American Society of Plant Biology, the Genetics Society of America and the International Plant Molecular Biology Society. Chandler has served on review panels for multiple federal funding agencies as well as on the editorial and advisory boards of numerous scientific publications.
Rebecca W. Doerge, PhD
Professor, Departments of Agronomy and Statistics, Purdue University
Rebecca W. Doerge has played an integral role in the establishment of Genomics at Purdue University and continues to forge new ground in the exciting areas of statistical genomics (also referred to as statistical bioinfomatics), quantitative genetics and bioinformatics.
Although Doerge’s formal training is in Mathematics and Statistics, her research lies on the interdisciplinary boundaries of many fields—including Animal Science, Biology, Biochemistry, Botany, Chemistry, Computer Science, Horticulture, Genetics, Genomics, Plant Breeding and others—that are currently involved in assessing genomic-based questions. Her current research encompasses four broad areas: developing a statistical methodology for genetic mapping and quantitative trait loci (QTL) location; applying up-to-date genetic mapping and (e-)QTL methodology to real experimental data; assessing genetic variation and diversity of populations and germplasm collections; and understanding and analyzing gene expression, protein expression and epigenomic data in order to statistically design and then test (epi-)genomic/biologically based questions.
Doerge has been employed at Purdue since 1995, where she holds a joint appointment between the Colleges of Agriculture and Science. Prior to joining Purdue, Doerge was a postdoctoral fellow at Cornell University. She received a doctorate in statistics from North Carolina State University and a master’s degree in mathematics from the University of Utah.
Since joining Purdue, Doerge has won many awards for both teaching and research, including Outstanding Assistant Professor for Excellence in Teaching and Research, Outstanding Teacher of Undergraduates in the School of Science, University Scholar, a Teaching for Tomorrow Award, and a College of Science Graduate Student Mentoring Award.
Doerge was promoted to associate professor of agronomy and statistics in 2000 and full professor of agronomy and statistics in 2003. In 2007, she became an elected a fellow of the American Statistical Association and an elected fellow of the American Association for the Advancement of Science.
Robert Last, PhD
Professor of Biochemistry and Molecular Biology and Plant Biology, College of Natural Sciences, Michigan State University
Robert Last is a geneticist who studies how plants make molecules that are nutritionally important to humans and provide protection against environmental stress. In recent years he has moved into using high throughput phenotypic functional genomics to understand complex biological processes such as chloroplast function and synthesis of complex natural products. This work requires generation and analysis of large datasets.
Last has worked in the public, private and government sectors. He advanced to Professor at The Boyce Thompson Institute for Plant Research at Cornell from 1989 to 1998, where his research focused on amino acid biosynthesis, UV-B tolerance mechanisms and vitamin C biosynthesis. He was a science director at Cereon Genomics LLC during the early days of plant genomics, where his group did discovery research for plant biotechnology at Monsanto. They did pioneering work in shotgun cloning of the Arabidopsis genome and used these data to create the first very large set of genetic markers for Arabidopsis. He was a Program Officer at the National Science Foundation from 2002 to 2004, where he was a member of the Plant Genomics Research Program, the Arabidopsis 2010 Working Group and The Interagency Microbial Sequencing Program Working Group.
Last has served the scientific community in a wide variety of ways. He has been on the editorial board of several journals, most notably as Associate Editor of Plant Physiology from 1999 to 2007. He taught the Arabidopsis Course at Cold Spring Harbor Laboratory for three years, starting in 1995. He was a member of the NAS/NRC Committee on the National Plant Genome Initiative from 2003 to 2008, and of the Keystone Symposia Scientific Advisory Board from 2001 to 2004. He served on the NIH Biological Sciences-1 Study Section from 1995 to 1999, as well as on National Science Foundation grant review panels. He currently serves on the Public Affairs Committee of the American Society of Plant Biologists and the Scientific Advisory Board of the EU-SOL functional genomics project.
Last received the NSF Presidential Young Investigator Award in 1990, and was named a Monsanto Fellow in 2002.
Nirav Merchant, PhD
Director, Biotechnology Computing Facility at the Arizona Research Laboratories (ARL), The University of Arizona
Dr. Merchant 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 the area of life sciences informatics. His team works closely with interdisciplinary research groups to translate and integrate novel concepts into production level tools, applications and turnkey solutions.
His research interests include high performance computing and storage, robotic laboratory automation, semantic data integration, and tools for remote collaboration --with a focus on adoption of emerging data analysis and visualization techniques to life sciences research questions. His group focuses on integration of technologies such as grid computing, reconfigurable computing architectures and virtualization for high throughput analysis frameworks.
He actively collaborates with campus and open source communities on implementing and adopting open standards for data management and data portability.
He volunteers with nonprofit organizations in India to develop improved and simplified health care delivery systems utilizing open source software.
Sudha Ram, PhD
McClelland Professor of Management Information Systems, Eller College of Management, The University of Arizona (UA)
Sudha Ram works in the area of enterprise data management, where she develops techniques to store, retrieve and manage data used by companies for both day-to-day operations and strategic decision-making. Her work focuses on providing semantic interoperability among disparate databases using methods such as machine learning, statistical approaches, ontologies and conceptual modeling. She developed the SCROL ontology and CREAM software system for integrating multiple heterogeneous databases. She has edited two volumes of books published by Springer Verlag and published more than 150 research articles for refereed journals, conferences and book chapters.
In the area of biological database integration, Ram has developed ontology-based mechanisms to dynamically link multiple gene, protein and functional databases. These mechanisms have been embedded into software tools as well. Her recent research, funded by the Library of Congress and the National Science Foundation (NSF), resulted in the development of the W7 model for data provenance; this model has been adopted by organizations such as Raytheon Missile Systems, SAP and Ford Motor Company.
She also has expertise in digital data archiving and preservation, and information life cycle management. She serves as a consultant to several Fortune 100 companies on data warehousing, business intelligence, data and metadata management, and information technology strategy. Her research has been funded by organizations such as IBM, Intel Corporation, SAP, Ford Motor Company, Raytheon Missile Systems, the U.S. Army, the National Institute of Standards and Technology, the NSF, NASA, and the Office of Research and Development of the CIA.
Ram serves as the senior editor for Information Systems Research, and she is on the editorial board for many leading Information Systems journals. She is a cofounder of the Workshop on Information Technology and Systems (WITS), and she has published articles in Communications of the ACM, IEEE Expert, IEEE Transactions on Knowledge and Data Engineering, Information Systems, Information Systems Research, Management Science, and MIS Quarterly.
Daniel Stanzione, PhD
Founding Director, Fulton High Performance Computing Institute (HPCI) at Arizona State University (ASU)
The 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.
Daniel Stanzione’s research includes a long-standing interest in the development of problem-solving environments to support scientists in using high-end computing resources.
In addition to providing supercomputing and storage facilities, Stanzione and his team work with researchers to aid in the scale-up of computational models, as well as connecting multiple models across disciplines and connecting models to large scale, interactive visualization through ASU’s Decision Theater (an immersive three-dimensional visualization facility).
Stanzione is a co-investigator with the Texas Advanced Computing Center in deploying the Ranger system, the first of the systems supported by National Science Foundation (NSF) Petascale Computing program, and the machine that will be the largest open computing system in the world. Stanzione and his team will support the national TeraGrid user community in accessing the machine and develop new training courses in petascale software development for this community.
Prior to arriving at ASU, Stanzione was a Science and Technology Policy Fellow for the American Association for the Advancement of Science at the NSF. He holds a doctorate and a master of science in computer engineering, and a bachelor’s of science degree in electrical engineering, all from Clemson University.
Ann E. Stapleton, PhD
Associate Professor, Department of Biology and Marine Biology, University of North Carolina at Wilmington (UNCW)
Ann 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 and her students employ physiological, gene expression and complex trait genetic tools to define how plants are affected by ultraviolet radiation and drought, and then use that information to design genetic screens for analyzing response pathways. Stapleton also has several interdisciplinary collaborations, ranging from bioinformatics software development to development of Bayesian statistical models.
She has been recognized as an outstanding mentor for under-represented minority students and was instrumental in development of the UNCW Center for Support of Undergraduate Research and Fellowships. She has served as a panel manager for the USDA’s Cooperative State Research, Education, and Extension Service, and she has reviewed for more than 20 journals.
Before joining the UNCW faculty, Stapleton did postdoctoral research at the University of North Carolina at Chapel Hill and at Stanford University; she also served on the faculty of the University of Tennessee at Chattanooga.
Stapleton has published articles in numerous journals, including the Proceedings of the National Academy of Sciences; Plant Physiology; Plant, Cell and Environment; the Journal of Photochemistry and Photobiology; Drug Discovery Today; the International Journal of Computer and Information Science; Marine Biology; Statistical Methodology; the Plant Journal; and Microbial Ecology.
Lincoln Stein, MD, PhD
Cold Spring Harbor Laboratory
Lincoln Stein is taking a proactive approach to the current "information explosion" in genomics. His lab is developing 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.
Stein developed and manages the “HapMap” database, a large set of human single nucleotide polymorphisms (SNPs) and their genotypes in three world populations. The information in this database allows for rapid identification of disease susceptibility and other genetically-determined traits.
He is also working on WormBase, a database of C. elegans' genome and biology that includes information on the organism's genes, genetic interactions, cellular anatomy, and nervous system. WormBase also gives users access to the large body of C. elegans literature.
Other projects include Gramene, a comparative mapping resource for rice and other monocots that will help researchers identify candidate genes of interest in maize, wheat, and other grains; and Reactome, an interactive database of fundamental human biological pathways.
He has published articles in Nature, Science, Nucleic Acids Research, PLoS Biology, and Genome Research.
