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

这个合作项目旨在建立一个国家计算资源，使研究界更接近于实现生命之树计划的目标，即重建所有生物的进化史。这个目标就是进化生物学的计算大挑战。目前的方法仅限于小几个数量级的问题，而且它们不能在其范围的高端提供足够的精度。计划中的资源将被设计成一个孵化器，以促进这项极具挑战性的计算任务的新想法的发展；它将为实验家、计算生物学家和计算机科学家创建一个论坛，以共享数据、比较方法和分析结果，从而加快工具开发，同时维持当前的生物研究项目。该资源将包括一个大型计算平台，一个可互操作的高性能系统发育分析软件集合，以及一个大型数据集数据库，包括真实的和模拟的，以及它们的分析；开发人员、研究人员和教育工作者可以通过任何Web浏览器访问它。该软件以源代码形式免费提供，可用于从笔记本电脑到高性能、支持网格的计算引擎（如该项目的平台）的各种规模，并将被打包以与当前流行的工具兼容。为了建立这一资源，该合作项目将支持系统信息学（存储带有详细注释的多层数据的数据库，并支持复杂的、面向树的查询）、优化算法、贝叶斯推理和用于系统发育重建的符号操作，以及在基因组水平上模拟分支进化的研究项目，所有这些都在虚拟协作中心的背景下进行。生物学，特别是系统发育学，在数据采集和分析方面几乎完全被现代信息技术重新定义了。系统发育学家已经制定了具体的模型和问题，现在可以使用最新的数据库技术和优化算法来解决。因此，生物学家和计算机科学家密切合作解决系统发育中的IT问题的时机正好，由于组合难度和总体规模的结合，其中许多问题需要新颖的方法。该项目的研究团队包括从事数据库、算法设计、算法工程和高性能计算的计算机科学家、进化生物学家和系统学家、生物信息学家和生物统计学家，他们有着成功合作的历史和基础贡献的记录，以提供所需的广度和深度。该项目将汇集来自许多领域的研究人员，并在计算生物学领域培养新型合作和新型研究；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的方向。随着更多的全基因组测序和收集到足够的数据来尝试推断生命之树，它将有助于创建未来几十年研究界将使用的计算基础设施。该项目将帮助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，以及生物学中的许多其他研究问题，最终导致生态学、药剂学、法医学和安全性方面的重大进展。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宣传进化论、基因组学和生物信息学。它还将激励高中生和大学生从事生物信息学方面的职业。该项目提供了一个非凡的机会，在科学中最令人兴奋的跨学科领域之一培养本科生和研究生以及博士后研究人员。合作机构为大量代表性不足的群体提供服务，并致力于增加他们对研究的参与。

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.