Extended Development of the CIPRES Science Gateway, a Resource for Biological Research.

项目概要/摘要。了解生物体的进化史是至关重要的 生物学和生物医学研究的各个领域。进化信息对发现过程至关重要 从蛋白质到种群的所有生物尺度。CIPRES科学网关（CIPRES）是一个全球性的 加速从DNA序列数据推断进化历史的资源。CIPRES提供公共 免费访问在高性能计算（HPC）资源上运行的社区遗传学软件， 用户. CIPRES允许研究人员有效地访问遗传学软件的所有功能， 一个浏览器界面，无需安装代码，学习插件的细节，并构造命令 线CIPRES是其中许多代码的唯一公共资源，完成分析的速度比 典型的笔记本电脑，允许用户同时运行许多分析，并提供无限的存储空间， 结果。目前，每月约有2，000名用户通过CIPRES提交20，000份工作; 在与NIH优先事项相关的主题领域产生了3，000多份同行评审的出版物， 从酶学到流行病学CIPRES为从艾滋病毒传播到 生命之树上一个全新分支的发现。所有这些发现都发生得更快，因为 CIPRES提供对HPC资源的轻松访问。这里提出的项目将改进用于 创建CIPRES，使其更有效，更容易访问。它将提供一个环境， 研究人员可以轻松地进行协作，有选择地共享数据，并公开他们的结果。它会暴露 通过包括Galaxy和Geneious在内的其他重要软件环境获得CIPRES服务。 该项目将增加一些用户要求的功能，以便工作更有效率，包括重新启动作业， 提前终止，传输大文件，输入文件验证，自动配置作业 以实现最佳执行。该项目将提供对许多已要求的新社区代码的访问， 以及在项目生命周期中出现的问题。界面的改进将使其更快，更直观， 并且可以在智能手机和平板电脑上使用。该项目还将为用户提供“云爆发”功能。用户 将能够在按服务收费的基础上或通过NIH Commons帐户向商业云提供商提交工作 当他们的工作对于标准CIPRES社区资源来说太大时。这种能力意味着CIPRES可以 可以为任何规模的用户群体无限期地扩展和维持。这些改进（包括 和计算能力）预计将大大增加将CIPRES纳入其 日常工作流程。这里所做的改进将通过以下方式提供给全球研究界： 将底层软件发布为可供任何社区使用的开源、可分发软件包 访问HPC资源的实践。因此，为CIPRES用户创建的所有改进都可以 在其他特定研究社区的其他在线资源中简单快速地实现。

Project Summary/Abstract. Understanding the evolutionary history of living organisms is of central importance to every field of biological and biomedical research. Evolutionary information is critical to the discovery process across all biological scales, from proteins to populations. The CIPRES Science Gateway (CIPRES) is a global resource that speeds up inference of evolutionary history from DNA sequence data. CIPRES provides public access to community phylogenetics software run on high performance computing (HPC) resources at no cost to the user. CIPRES allows investigators to access all the capabilities of phylogenetics software efficiently though a browser interface, without having to install the codes, learn the details of schedulers, and construct command lines. CIPRES is the sole public resource for many of these codes, completes analyses 5-30 fold faster than a typical laptop computer, allows users to run many analyses simultaneously, and provides indefinite storage of the results. At present, approximately 2,000 users per month submit 20,000 jobs through CIPRES; they have produced more than 3,000 peer reviewed publications in subject areas relevant to NIH priorities, from enzymology to epidemiology. CIPRES has provided support for research ranging from HIV virus transmission to the discovery of an entire new branch in the tree of life. All of these discoveries happen more quickly because CIPRES provides easy access to HPC resources. The project proposed here will improve the software used to create CIPRES, making it more effective and easier to access. It will provide an environment that allows researchers to easily collaborate, share data selectively, and make their results publicly available. It will expose access to CIPRES services through other important software environments, including Galaxy and Geneious. The project will add a number of user-requested features so work is more efficient, including restarting jobs that have terminated prematurely, transferring large files, and input file validation with automatic configuration of jobs for optimal execution. The project will provide access to many new community codes that have been requested, and those that appear during the project lifetime. Improvements to the interface will make it faster, more intuitive, and useable on smart phones and tablets. The project will also give users “cloud-bursting” capabilities. Users will be able to submit jobs to a commercial cloud provider on a fee-for-service basis or via NIH commons account when their job is too large for the standard CIPRES community resources. This capability means CIPRES can be scaled and sustained indefinitely for a user population of any size. These improvements (both in capabilities and compute capacity) are expected to greatly expand the number of users who incorporate CIPRES into their day-to-day workflow. The improvements made here will be available to the global research community through release of the underlying software as an open source, distributable package that can be used by any community of practice to access HPC resources. As a result, all improvements created for CIPRES users can be implemented simply and quickly in other online resources for other specific research communities.