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 National Center for Earth-surface Dynamics (NCED) is a Science and Technology Center focused on understanding the processes that shape the Earth's surface, and on communicating that understanding with a broad range of stakeholders. NCED's work will support a larger, community-based effort to develop a suite of quantitative models of the Earth's surface: a Community Sediment Model (CSM). Results of the NCED-CSM collaboration will be used for both short-term prediction of surface response to natural and anthropogenic change and long-term interpretation of how past conditions are recorded in landscapes and sedimentary strata. This will in turn help solve pressing societal problems such as estimation and mitigation of landscape-related risk; responsible management of landscape resources including forests, agricultural, and recreational areas; forecasting landscape response to possible climatic and other changes; and wise development of resources like groundwater and hydrocarbons that are hosted in buried sediments. NCED education and knowledge transfer programs include exhibits and educational programs at the Science Museum of Minnesota, internships and programs for students from tribal colleges and other underrepresented populations, and research opportunities for participants from outside core NCED institutions. The Earth's surface is the dynamic interface among the lithosphere, hydrosphere, biosphere, and atmosphere. It is intimately interwoven with the life that inhabits it. Surface processes span environments ranging from high mountains to the deep ocean and time scales from fractions of a second to millions of years. Because of this range in forms, processes, and scales, the study of surface dynamics has involved many disciplines and approaches. A major goal of NCED is to foster the development of a unified, quantitative science of Earth-surface dynamics that combines efforts in geomorphology, civil engineering, biology, sedimentary geology, oceanography, and geophysics. Our research program has four major themes: (1) landscape evolution, (2) basin evolution, (3) biological sediment dynamics, and (4) integration of morphodynamic processes across environments and scales. Each theme area provides opportunities for exchange of information and ideas with a wide range of stakeholders, including teachers and learners at all levels; researchers, managers, and policy makers in both the commercial and public sectors; and the general public.
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TEAM MEMBERS:
Efi Foufoula-GeorgiouChristopher PaolaGary Parker
The California Academy of Sciences will produce "Water is Life," a 30,383 square-foot permanent exhibit with educational programming. The exhibit is designed to engage the public with the living world of water, to foster environmental stewardship and increase science literacy. Three habitat components -- Philippine Coral Reef, California Coast and Global Rainforests -- are conceptually and experientially linked through "Water Planet," which explores water's physical properties and how they impact living organisms and lead to aquatic diversity. Each component also reinforces the importance of conserving aquatic resources. Educational programming takes "Water is Life" to local schools and community events and onto the World Wide Web, as well as provides venues for formative evaluation of exhibit design elements. The development of lending kits, plus supporting manuals and workshops, will extend the reach of "Water is Life" regionally and nationally. Similarly, instruction manuals and workshops for creating desktop, living reefs will have national impact. The compelling draw of live organisms, hands-on activities, and exhibit enrichment through educational programming provide accessibility to a large, diverse audience. The exhibit will reach over one million annual visitors, and a larger audience will experience distributed educational programs.
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TEAM MEMBERS:
Margaret BurkeLinda KulikChristopher AndrewsTerrence GoslinerRobert Jenkins