The problem of accessing data is as old as science itself. Complete popularisation of scientific data (of a theoretical model), and even more so of the methods and materials used during an experimental process and of the empirical data amassed, has always been considered an essential part of the process of authentication, duplication and filing of scientific knowledge. It is also true, however, that this theory has always been a complex riddle with no simple solution. Strangely enough, in today's era of instant communication, the challenge of information access seems to be facing new, daunting
This collaborative project aims to establish a national computational resource to move the research community much closer to the realization of the goal of the Tree of Life initiative, namely, to reconstruct the evolutionary history of all organisms. This goal is the computational Grand Challenge of evolutionary biology. Current methods are limited to problems several orders of magnitude smaller, and they fail to provide sufficient accuracy at the high end of their range. The planned resource will be designed as an incubator to promote the development of new ideas for this enormously challenging computational task; it will create a forum for experimentalists, computational biologists, and computer scientists to share data, compare methods, and analyze results, thereby speeding up tool development while also sustaining current biological research projects. The resource will be composed of a large computational platform, a collection of interoperable high-performance software for phylogenetic analysis, and a large database of datasets, both real and simulated, and their analyses; it will be accessible through any Web browser by developers, researchers, and educators. The software, freely available in source form, will be usable on scales varying from laptops to high-performance, Grid-enabled, compute engines such as this project's platform, and will be packaged to be compatible with current popular tools. In order to build this resource, this collaborative project will support research programs in phyloinformatics (databases to store multilevel data with detailed annotations and to support complex, tree-oriented queries), in optimization algorithms, Bayesian inference, and symbolic manipulation for phylogeny reconstruction, and in simulation of branching evolution at the genomic level, all within the context of a virtual collaborative center. Biology, and phylogeny in particular, have been almost completely redefined by modern information technology, both in terms of data acquisition and in terms of analysis. Phylogeneticists have formulated specific models and questions that can now be addressed using recent advances in database technology and optimization algorithms. The time is thus exactly right for a close collaboration of biologists and computer scientists to address the IT issues in phylogenetics, many of which call for novel approaches, due to a combination of combinatorial difficulty and overall scale. The project research team includes computer scientists working in databases, algorithm design, algorithm engineering, and high-performance computing, evolutionary biologists and systematists, bioinformaticians, and biostatisticians, with a history of successful collaboration and a record of fundamental contributions, to provide the required breadth and depth. This project will bring together researchers from many areas and foster new types of collaborations and new styles of research in computational biology; moreover, the interaction of algorithms, databases, modeling, and biology will give new impetus and new directions in each area. It will help create the computational infrastructure that the research community will use over the next decades, as more whole genomes are sequenced and enough data are collected to attempt the inference of the Tree of Life. The project will help evolutionary biologists understand the mechanisms of evolution, the relationships among evolution, structure, and function of biomolecules, and a host of other research problems in biology, eventually leading to major progress in ecology, pharmaceutics, forensics, and security. The project will publicize evolution, genomics, and bioinformatics through informal education programs at museum partners of the collaborating institutions. It also will motivate high-school students and college undergraduates to pursue careers in bioinformatics. The project provides an extraordinary opportunity to train students, both undergraduate and graduate, as well as postdoctoral researchers, in one of the most exciting interdisciplinary areas in science. The collaborating institutions serve a large number of underrepresented groups and are committed to increasing their participation in research.
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TEAM MEMBERS:
Tandy WarnowDavid HillisLauren MeyersDaniel MirankerWarren Hunt, Jr.
The "Salmon Research Team: A Native American Technology, Research and Science Career Exposure Program" is a three-year, youth-based ITEST project submitted by the Oregon Museum of Science and Industry. The project seeks to provide advanced information technology and natural science career exposure and training to 180 middle level and high school students. Mostly first-generation college-bound students, the target audience represents the Native American community and those with Native American affiliations in reservation, rural and urban areas. Students will investigate computer modeling of complex ecological, hydrological and geological problems associated with salmon recovery efforts. Field experiences will be provided in three states: Oregon, Washington and northern California. The participation of elders and tribal researchers will serve as a bridge between advanced scientific technology and traditional ecological knowledge to explore sustainable land management strategies. Students will work closely with Native American and other scientists and resource managers throughout the Northwest who use advanced technologies in salmon recovery efforts. Student participation in IT-dependent science enrichment and research activities involving natural science fields of investigation will occur year round. Middle school students are expected to receive at least 330 contact hours including a one-week summer research experience, a one-week spring break program, and seven weekends of residential programs during the school year. The high school component consists of 460 contact hours reflecting one additional week for the summer research experience. In addition to watershed and salmon recovery related research, students will be involved in other ancillary research projects. A vast array of partners are positioned to support the field research experience including, for example, the U.S. Department of the Interior, Redwood National State Park, College of Natural Resources and Sciences at Humboldt State University, Confederated Tribes of the Warm Springs, University of Oregon Institute of Marine Biology, University of Washington Columbia Basin Research project, the Northwest Center for Sustainable Resources at Chemeketa Community College and the Integrated Natural Resource Technology program at Mt. Hood Community College. The project is intended to serve as a model for IT-based youth science programs that address national and state education standards and are relevant to the cultural experience of Native American students. Two mentors will provide continued support to students: an academic mentor at the student's schools and a professional mentor from a local university or natural resource agency. Incentives will be provided for student participation including stipends and internships. Career exposure and work-related skills are integrated throughout the project activities and every program component. Creative strategies are used to encourage family involvement including, for example, salmon bakes and museum discounts.
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TEAM MEMBERS:
Travis Southworth-NeumeyerDaniel Calvert
The Educational Broadcasting Corporation (WNET in New York) is developing and producing a new public television project exploring cutting-edge technology. The project consists of an eight-part hourly broadcast component; six 60-second "mini-programs;" a World Wide Web component; and extensive educational outreach targeted to adults aged 25-39 and older. The topics for the eight programs in season one are: Replacements - prosthetic devices and biologically electronic artificial body parts In Search of Eve - the race to decode the human genome Light of the 21st Century - Fiber Optics Nanotechnology - molecular manipulation of materials Technospy - technologies used to gain information Sports Technology - the pursuit of better equipment and training regimes Artificial Intelligence - efforts to create computers the mimic human intelligence Appropriate Technologies - technologies that use local, inexpensive material Beth Hoppe, WNET's Director of Science Programs will serve as Executive Producer for the series. Each of the programs would be produced by an independent producer selected by WNET. Content advisors include: Angela Christiano, Departments of Dermatology, Genetics and Development, Columbia University; Sheila Sen Jasanoff, Harvard University JFK School of Government; Horace Freeland Judson, Center for History of Recent Science, George Washington University; Michio Kaku, theoretical physicist, CUNY and host, Explorations radio series; Wilfred Pinfold, Microprocessor Research Labs, Intel Corp.; and Barbara Wilson, chief technologist, NASA's Jet Propulsion Laboratory
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TEAM MEMBERS:
Beth HoppeTamara RobinsonWilliam GrantBarbara Flagg