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（La Jolla， CA）因创建CIPRES REST API （CRA）而获得ABI开发奖，这是一套为生物界提供的公共网络服务。CRA将使任何具有适度编程技能的生物学家能够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嵌入到8个不同的软件环境中，这些软件环境广泛应用于生物界，提供从这些熟悉的工作环境中直接访问超级计算资源的途径。CRA将使科学家能够在不改变正常工作环境或学习使用新软件的情况下，分析比目前可能的更大的数据集。社区开发人员将能够以新的和创造性的方式将CRA工具合并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，这是一个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。在运行的头30个月里，CIPRES科学门户已经为5000多名用户进行了分析，使400多份生物学学科的学术出版物得以发表，从生态学到病毒学，至少有68名教师使用它来教授课程。CIPRES科学门户原型的影响是深远的，因为了解生物体的进化史是所有生物研究领域的核心，而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。目前，DNA和蛋白质序列获取的速度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，但它也意味着常规分析不能再用笔记本电脑或台式电脑进行。研究人员必须能够方便地访问高性能计算（HPC）资源来参与发现过程。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，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。所创建的软件和技术将是完全通用的，并且很容易适应任何科学领域，这些领域的进步受到计算资源访问的限制。有关该项目的更多信息可从http://www.phylo.org/index.php/portal/或mmiller@sdsc.edu获得。

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.