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 X-Tech program will bring together the Exploratorium and staff at five Beacon Centers to create an innovative technology program using STEM and IT activities previously tested at the Exploratorium. At each X-Tech Club, two Beacon Center staff and two Exploratorium Youth Facilitators will work with 20 middle school students each year for a total of 300 participants. Youth Facilitators are alumni of the Exploratorium's successful Explainer program and will receive 120 hours of training in preparation for peer mentoring. Each site will use the X-Tech hands-on curriculum that will focus on small technological devices to explore natural phenomenon, in addition to digital imaging, visual perception and the physiology of eyes. Parental involvement will be fostered through opportunities to participate in lectures, field trips and open houses, while staff at Beacon Centers will participate in 20 hours of professional development each year.
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TEAM MEMBERS:
Vivian AltmannDarlene LibreroVirginia WittMichael Funk
WNET is producing "The Human Spark," a multimedia project that includes a four-part television series (4 x 60 min) for national primetime broadcast on PBS, innovative outreach partnerships with museums, an extensive Web site and outreach activities, including a Spanish-language version and companion book. Hosted by Alan Alda, "The Human Spark" will explore the intriguing questions: What makes us human? Can the human spark be found in the differences between us and our closest genetic relative -- the great apes? Is there some place or process unique to the human brain where the human spark resides? And if we can identify it, could we transfer it to machines? The programs will explore these questions through presenting cutting-edge research in a number of scientific disciplines including evolution, genetics, cognitive neuroscience, behavioral science, anthropology, linguistics, AI, robotics and computing. The series will highlight opposing views within each field, and the interdisciplinary nature of science, including its intersection with the humanities. The series will develop a new innovative format, the "muse concept", which involves pairing the host with a different scientific expert throughout each program. The outreach plan is being developed with a consortium of four leading science museums, American Museum of Natural History in New York, Museum of Science in Boston, The Exploratorium in San Francisco, and the Fort Worth Museum of Science and History, paired with their respective local public television stations. An additional six museums and local broadcasters will be chosen through an RFP process to develop local initiatives around the series. Multimedia Research and Leflein Associates will conduct formative as well as summative evaluations of the series and web.
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TEAM MEMBERS:
William GrantJared LipworthGraham CheddBarbara Flagg
The Ocean Institute (OI), in partnership with Scripps Institution of Oceanography (Scripps), Capistrano Valley Boys & Girls Clubs (BGC) and the Institute of Electrical and Electronics Engineers (IEEE), is developing "SeaTech," a multi-year, Youth-based ITEST program providing 120 female and minority middle and high school students from underserved populations with 391 contact hours of information technology (IT)-intensive oceanographic research experiences. SeaTech content focuses on understanding the acoustic behaviors of whales and dolphins, specifically, sound production, noise impacts and acoustic population census in California, the Bering Sea and the Southern Ocean. SeaTech offers a two-year core program for 13 & 14 year olds consisting of a "Breadth of Exposure" phase and a "Depth of Skills" phase totaling 299 hours. The core program has three distinct elements -- after-school clubs, field explorations and summer research institutes -- and is augmented with efforts before and after: an Early Pipeline Development phase (52 hours) for youth age 12, and Internships (40 hours) for youth age 15. The three-year ITEST grant will host three cohorts of 40 participants each. Each youth participant will receive 391 total contact hours. Through efforts directed at parents, SeaTech anticipates involving 60 parents in about 80 hours of activities each year. Coordinated through and with the expertise of Capistrano Valley BGC, recruitment will include orientation and information programs, a bilingual brochure and direct efforts by BGC staff. In addition, recruitment will happen from local schools. INTELLECTUAL MERIT: IT-based studies of marine mammal bio-acoustics will 'hook' student interest in after-school clubs, field explorations and summer research institutes. SeaTech advances understanding of the role of broader pipeline development in addressing chronic recruitment and retention problems in teen-targeted IT programs. BROADER IMPACTS: SeaTech programming has been meticulously and demonstrably integrated into the afterschool programming at the BGC. The SeaTech Club provides organizational structure to the teen activities at the BGC; however, the IT curriculum is also integrated into two nationally renowned extant structures called Career Launch and Club Tech. Findings from the project's examination of recruitment, retention and parental involvement will have broad implications to the field of informal science education.
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TEAM MEMBERS:
Harry HellingKelly ReynoldsJohn HildebrandCandice Dickens