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.
SRI and Girls, Inc. of Alameda County will develop a problem-based program for underserved middle-school girls. "Build IT" will serve 300 girls in three years providing each with 150 contact hours of programming. The program is designed to increase IT fluency, motivate girls to engage in IT related activities, encourage the pursuit of IT careers and increase interest in mathematics. Participants will progress through three stages: Apprentice, Journeygirl, and Specialist. Apprentices learn how to use Internet communication tools and interact with design professionals in a variety of IT fields. Journeygirls engage in software design and create small mobile devices while working in conjunction with software engineers in Stanford University's Learning, Design, and Technology Program. Specialists continue to work in design teams and build valuable project and resource management skills. A curriculum will be developed that builds on NSF-funded products such as Techbridge (HRD 00-80386) and Imagination Place (HRD 97-14749), while addressing communication technologies, networking, wireless and mobile communication tools, web development and computer programming. Troubleshooting and leadership skills will also be included. Additional activities consist of professional development for Girls, Inc. staff to build IT fluency, as well as Family Tech Nights to encourage parental involvement.
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TEAM MEMBERS:
Melissa KochMelissa BryanMarie BienkowskiDeborah Emery
This project develops an 8-week middle-school mathematics module that introduces cryptography, the science of sending secret messages, while teaching and reinforcing the learning of related mathematical concepts. The topics range from the classical encryption systems and the historic context in which they were used through powerful modern encryption systems that provide secrecy in electronic messages today. The module also covers passwords and codes that correct errors in the transmission of information. Public awareness of the importance of cryptography is growing, as is the need to understand the issues involved. The study of cryptography provides an interesting context for students to apply traditional mathematical skills and concepts. Mathematical topics covered include percents, probability, functions, prime numbers, decimals, inverses and modular arithmetic. The main product is a middle-school student book, with accompanying teacher materials. A web site is being developed that supports the activities in this book. Abbreviated modules for Grades 3, 4 and 5 are also being developed, as well as an instructor's guide for adapting the materials for use in informal educational settings such as museums and after-school programs. The development of the module involves piloting and field-testing by experienced classroom teachers from diverse school communities and instructors of informal educational programs. Evaluation includes review by mathematicians and educators, as well as an investigation into the level of students' understanding of the topics studied.