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

CIPRES 科学网关的扩展开发，生物研究资源。

• 批准号: 10184825
• 负责人: MARK A MILLER
• 金额: $ 2.63万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-12-15 至 2021-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10184825
• 关键词: Algorithmic Software; Archives; Area; Basic Science; Biological; Biology; Biomedical Research; Cellular Phone; Cloud Service; Code; Communities; Community of Practice; Complement; Computer software; Computers; DNA Sequence; DNA sequencing; Data; Data Analyses; Development; Discipline; Ensure; Environment; Enzymatic Biochemistry; Epidemiology; Fee-for-Service Plans; Future; Galaxy; Genetic; Genome; Genomics; HIV; Health; Health Services Accessibility; High Performance Computing; Hour; Human; Infrastructure; Internet; Intuition; Journals; Learning; Life; Modernization; Molecular Biology; Occupations; Organism; Outcome; Peer Review; Performance; Phylogenetic Analysis; Population; Population Biology; Population Genetics; Privatization; Process; Proteins; Provider; Publications; Publishing; Recording of previous events; Reproducibility of Results; Research; Research Personnel; Research Support; Resources; Running; Schedule; Science; Scientist; Sequence Alignment; Services; Software Tools; Speed; Tablets; Technology; Time; Trees; United States National Institutes of Health; Update; Validation; Virus; Work; base; biological research; cluster computing; computing resources; cost; data acquisition; data sharing; digital; flexibility; graphical user interface; handheld mobile device; improved; innovation; laptop; large datasets; light weight; online resource; open source; precision medicine; premature; programs; real time monitoring; service providers; software infrastructure; supercomputer; tool; user-friendly; viral transmission; virology; web portal; web services

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.

项目摘要/摘要。了解生物体的进化史至关重要。 对于生物和生物医学研究的每个领域，进化信息对于发现过程都至关重要。 CIPRES 科学网关 (CIPRES) 涵盖所有生物尺度，从蛋白质到种群。 CIPRES 向公众提供了加速从 DNA 序列数据推断历史进化的资源。 免费访问在高性能计算 (HPC) 资源上运行的社区系统发育软件 CIPRES 允许研究人员有效地访问系统发育软件的所有功能。 浏览器界面，无需安装代码，无需了解调度程序的详细信息，无需构建命令 CIPRES 是其中许多代码的唯一公共资源，完成分析的速度比其他代码快 5-30 倍 典型的笔记本电脑，允许用户同时运行许多分析，并提供无限期的存储 目前，每月约有 2,000 名用户通过 CIPRES 提交 20,000 个职位； 在与 NIH 优先事项相关的学科领域发表了 3,000 多份同行评审出版物， CIPRES 为从 HIV 病毒传播到流行病学的研究提供了支持。 生命之树上全新分支的发现 所有这些发现发生得更快，因为 CIPRES 提供对 HPC 资源的轻松访问，此处提出的项目将改进用于 HPC 资源的软件。 创建 CIPRES，使其更有效且更易于访问，它将提供一个允许的环境。 研究人员可以轻松地进行协作，有选择地共享数据，并将其结果公开。 通过其他重要的软件环境（包括 Galaxy 和 Geneious）访问 CIPRES 服务。 该项目将添加许多用户请求的功能，使工作更加高效，包括重新启动作业 提前终止、传输大文件以及通过自动配置作业进行输入文件验证 为了实现最佳执行，该项目将提供对所请求的许多新社区代码的访问， 以及在项目生命周期中出现的界面改进将使其更快、更直观， 该项目还将为用户提供“云爆发”功能。 将能够按服务收费或通过 NIH commons 帐户向商业云提供商提交作业 当他们的工作对于标准 CIPRES 社区资源来说太大时，此功能意味着 CIPRES 可以。 对于任何规模的用户群体都可以无限期地扩展和维持。 和计算能力）预计将大大增加将 CIPRES 纳入其应用的用户数量 日常工作流程中所做的改进将通过以下方式提供给全球研究界。 将底层软件作为开源、可分发的软件包发布，可供任何社区使用 因此，为 CIPRES 用户创建的所有改进都可以实现。 在其他特定研究社区的其他在线资源中简单快速地实施。