Information Technology Research (ITR): Building the Tree of Life -- A National Resource for Phyloinformatics and Computational Phylogenetics

信息技术研究（ITR）：构建生命之树——系统信息学和计算系统发育学的国家资源

• 批准号: 0331494
• 负责人: Satish Rao
• 金额: $ 122.97万
• 依托单位: University of California-Berkeley
• 依托单位国家: 美国
• 项目类别: Cooperative Agreement
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-10-01 至 2008-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0331494&HistoricalAwards=false
• 关键词: Information; Technology; Research; ITR; Building

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.

这个协作项目旨在建立国家计算资源，以使研究界更接近实现生命之树计划的目标，即重建所有生物的进化历史。这个目标是进化生物学的计算巨大挑战。当前的方法仅限于几个数量级的问题，并且在其范围的高端无法提供足够的准确性。计划的资源将被设计为孵化器，以促进这项极具挑战性的计算任务的新想法的发展； 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;开发人员，研究人员和教育工作者将通过任何网络浏览器访问它。该软件以源形式免费提供，可在从笔记本电脑到高性能，启用网格的计算机（例如该项目平台）的尺度上使用，并将包装与当前流行工具兼容。为了建立此资源，该协作项目将支持植链形式学的研究计划（数据库（数据库存储具有详细注释的多层次数据，以支持复杂的，面向树的查询），优化算法，贝叶斯推论，贝叶斯推论和符号的符号性和符号性操纵，以进行系统性的级别，并在基金会方面进行了仿真，并在基金会中进行了仿真，该级别的方向是所有的，这些方面的方面是所有的，以及在基金会方面的仿真级别，以及在所有方面均具有所有的态度，以实现所有范围，以实现所有的态度，以实现所有的态度，以实现所有的态度，以实现所有的态度，以实现所有的态度，以实现所有的态度，并在所有方面进行了整理，并且在整个级别的方面，在整个方面都在整个方面进行了任何级别的方面的态度。尤其是在数据获取和分析方面，中心生物学，尤其是系统发育，几乎已经被现代信息技术完全重新定义。系统发育学家已经提出了特定的模型和问题，这些模型和问题现在可以使用数据库技术和优化算法的最新进展来解决。因此，当生物学家和计算机科学家的密切合作解决系统发育问题的IT问题的时间完全正确，由于组合难度和整体规模的结合，许多人都要求采用新颖的方法。项目研究团队包括在数据库中工作的计算机科学家，算法设计，算法工程以及高性能计算，进化生物学家和系统主义者和系统主义者，生物信息学家和生物阶级主义者，并具有成功的合作历史，并提供了一些基本贡献的记录，以提供许多领域的研究，以提供新的研究和新设计的研究。计算生物学；此外，算法，数据库，建模和生物学的相互作用将为每个领域提供新的动力和新方向。 它将有助于创建研究界将在未来几十年中使用的计算基础架构，因为对更多的整个基因组进行了测序，并收集了足够的数据来尝试推断生命之树。该项目将有助于进化生物学家了解进化的机制，生物分子的进化，结构和功能之间的关系以及生物学的其他许多研究问题，最终导致了生态学，药物，取证和安全性的重大进展。该项目将通过合作机构的博物馆合作伙伴的非正式教育计划来宣传进化，基因组学和生物信息学。它还将激励高中生和大学大学生从事生物信息学的职业。该项目为培训科学最令人兴奋的跨学科领域之一的学生提供了一个非凡的机会，包括本科生和研究生以及博士后研究人员。协作机构为大量代表性不足的群体提供服务，并致力于增加他们参与研究。