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

加州大学圣地亚哥分校(加利福尼亚州拉荷亚)获得了ABI开发奖，以创建CIPRES REST API(CRA)，这是一套使生物界能够使用的公共Web服务。CRA将使任何具有一般编程技能的生物学家都可以在他们喜欢的工作环境中访问和运行NSF XSEDE超级计算机上强大的系统发育工具。该项目将把CRA嵌入生物界广泛使用的八个不同的软件环境中，提供从这些熟悉的工作环境中直接访问超级计算资源的能力。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工具整合到他们的软件环境中。该项目创建的工具是CIPRES科学网关原型的扩展，CIPRES科学网关是一个网络应用程序，允许研究人员通过标准浏览器界面对NSF XSEDE计算资源进行大型系统发育分析。在运行的头30个月里，CIPRES科学网关已经为5000多名用户运行了分析，支持了从生态学到病毒学的400多种生物学学科的学术出版物，并被至少68名教师用于课程交付。CIPRES科学网关原型的影响是深远的，因为理解活生物的进化史是生物学研究的所有领域的核心，进化关系主要是通过使用计算密集型算法比较DNA和蛋白质序列来探索的。DNA和蛋白质序列的获取速度目前比摩尔定律增长得更快。虽然这是澄清进化关系的一个前所未有的机会，但它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科学门户的僵化浏览器模式转变为普适访问模式来提高获取计算资源的效率，在这种模式下，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。创建的软件和技术将是完全通用的，很容易适应任何进展受到计算资源访问限制的科学领域。有关该项目的更多信息，请访问http://www.phylo.org/index.php/portal/或发送电子邮件至mmiler@sdsc.edu。

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 mmiller@sdsc.edu.