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。了解生物的进化史是至关重要的。 生物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 跨越所有生物尺度，从蛋白质到种群。CIPRES科学门户(CIPRES)是一个全球 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)资源上运行的社区系统发育软件 用户。然而，CIPRES允许研究人员高效地访问系统发育软件的所有功能 一个浏览器界面，无需安装代码，即可了解调度程序的详细信息，并构造命令 台词。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，允许用户同时运行多个分析，并提供无限存储 结果。目前，每月约有2,000名用户通过CIPRES提交20,000个工作；他们有 在与NIH优先事项相关的主题领域制作了3000多份同行评议的出版物，来自 从酶学到流行病学。CIPRES为从艾滋病毒传播到 在生命之树上发现了一个全新的分支。所有这些发现都发生得更快，因为 CIPRES提供了对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、更易于访问。它将提供一个环境，允许 研究人员可以轻松协作，有选择地共享数据，并将他们的结果公开。它会暴露出 通过包括Galaxy和Geneious在内的其他重要软件环境访问CIPRES服务。 该项目将添加许多用户请求的功能，以便工作更高效，包括重新启动以下作业 过早终止，传输大文件，并使用作业的自动配置进行输入文件验证 以达到最佳执行效果。该项目将提供对已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那些。对界面的改进将使其更快、更直观、 并可在智能手机和平板电脑上使用。该项目还将为用户提供“云爆破”能力。用户 将能够以按服务收费的方式或通过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的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。这些改进(在功能方面 和计算能力)预计将极大地扩大将CIPRES整合到其 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、可分发的包 访问高性能计算资源的实践。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而快速地实施。