ABI: Development: Bringing Supercomputing to the Desktop: New Capabilities for Phylogenetic Inference in the Era of Data-Driven Biology

ABI：发展：将超级计算带到桌面：数据驱动生物学时代系统发育推断的新功能

• 批准号: 1262628
• 负责人: Mark Miller
• 金额: $ 159.4万
• 依托单位: University of California-San Diego
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-05-01 至 2017-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1262628&HistoricalAwards=false
• 关键词: ABI; Development; Bringing; Supercomputing; Desktop

The University of California, San Diego (La Jolla, CA) has received an ABI development award to create the CIPRES REST API (CRA), a set of enabling public web services for the biology community. The CRA will make it possible for any biologist with modest programming skills to access and run powerful phylogenetic tools on NSF XSEDE supercomputers from within their preferred work environment. The project will embed the CRA into eight distinct software environments that are widely used in the biology community, providing direct access to supercomputing resources from within these familiar working environments. The CRA will make it possible for scientists to analyze much larger data sets than is currently possible without changing their normal work environment or learning to use new software. Community developers will be able to incorporate the CRA tools into their software environments in new and creative ways. The tools created by this project are an extension of the prototype CIPRES Science Gateway, a web application that allows researchers to run large phylogenetic analyses on NSF XSEDE computing resources through a standard browser interface. In its first 30 months of operation, the CIPRES Science Gateway has run analyses for more than 5,000 users, enabled 400+ scholarly publications in biological disciplines ranging from Ecology to Virology, and was used by at least 68 instructors for curriculum delivery.The impact of CIPRES Science Gateway prototype has been profound because understanding the evolutionary history of living organisms is central to all fields of biological research, and evolutionary relationships are explored primarily by comparing DNA and protein sequences using computationally intensive algorithms. The rate of DNA and protein sequence acquisition is currently increasing more rapidly than Moore's law. While this represents an unprecedented opportunity to clarify evolutionary relationships, it also means routine analyses can no longer be conducted with laptop/desktop computers. Researchers must have easy access to high performance computing (HPC) resources to participate in the discovery process. The CRA will improve the efficiency of access to computational resources by shifting from the rigid browser paradigm of the CIPRES Science Gateway to a pervasive access model, where the phylogenetic tools required for modern biological research are available from within the researcher's preferred environment. The software and techniques created will be completely generic and easily adapted to any area of science where progress is limited by access to computational resources. More information about this project can be obtained from http://www.phylo.org/index.php/portal/ or [e-mail].

位于圣地亚哥的加州大学（拉霍亚，CA）获得了ABI开发奖，以创建CIPRES REST API（CRA），这是一组为生物学社区提供的公共Web服务。CRA将使任何具有适度编程技能的生物学家都可以从他们首选的工作环境中访问并在NSF XSEDE超级计算机上运行强大的系统发育工具。该项目将把CRA嵌入到生物界广泛使用的八个不同的软件环境中，从这些熟悉的工作环境中直接访问超级计算资源。CRA将使科学家能够分析比目前更大的数据集，而无需改变他们的正常工作环境或学习使用新软件。社区开发人员将能够以新的和创造性的方式将CRA工具纳入他们的软件环境。该项目创建的工具是原型CIPRES Science Gateway的扩展，CIPRES Science Gateway是一个Web应用程序，允许研究人员通过标准浏览器界面在NSF XSEDE计算资源上运行大型系统发育分析。在其运营的前30个月，CIPRES科学网关已经为5,000多名用户进行了分析，使400多个生物学科的学术出版物，从生态学到病毒学，CIPRES科学网关原型的影响是深远的，因为了解生物体的进化历史是所有领域的核心，生物学研究和进化关系主要通过使用计算密集型算法比较DNA和蛋白质序列来探索。DNA和蛋白质序列获取的速率目前比摩尔定律增长得更快。虽然这代表了一个前所未有的机会来澄清进化关系，但这也意味着不能再用笔记本电脑/台式电脑进行常规分析。 研究人员必须能够轻松访问高性能计算（HPC）资源，才能参与发现过程。CRA将通过从CIPRES科学网关的严格浏览器范式转变为普遍访问模型来提高访问计算资源的效率，其中现代生物学研究所需的系统发育工具可以从研究人员首选的环境中获得。所创建的软件和技术将是完全通用的，并且很容易适用于任何科学领域，其中进展受到计算资源的限制。关于这个项目的更多信息可以从http://www.phylo.org/index.php/portal/或[e-mail]获得。