HyPhy: comprehensive, fast, and user-friendly software for evolutionary analysis

HyPhy：全面、快速且用户友好的进化分析软件

• 批准号: 8886417
• 负责人: Spencer V. Muse
• 金额: $ 38.49万
• 依托单位: TEMPLE UNIV OF THE COMMONWEALTH
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-15 至 2019-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8886417
• 关键词: 17 year old; Adoption; Algorithms; Amino Acids; Back; Big Data; Biomedical Research; Book Chapters; Cellular Phone; Client; Code; Codon Nucleotides; Collection; Communication; Complex; Computer software; Computers; DNA; Data; Data Analyses; Data Set; Development; Devices; Dinosaurs; Disease; Drug resistance; Educational workshop; Elements; Engineering; Ensure; Figs - dietary; Funding; Genes; Human; Imagery; Immune; Immune response; Immunology; Internet; Language; Learning; Letters; Libraries; Library Services; Marketing; Methods; Mind; Modeling; Molecular; Molecular Sequence Data; Monkeys; Mutation; National Institute of General Medical Sciences; Occupations; Peer Review; Penetration; Performance; Phylogenetic Analysis; Plug-in; Population; Positioning Attribute; Problem Solving; Procedures; Productivity; Protocols documentation; Publications; RNA; Research Infrastructure; Research Personnel; Resources; Running; Software Engineering; System; Technology; Time; Viral; Work; base; cloud based; comparative; computerized tools; data exchange; design; experience; flexibility; graphical user interface; handheld mobile device; improved; innovation; microbial; molecular domain; open source; operation; pathogen; portability; pressure; programs; protein structure function; public health relevance; software development; user friendly software; user-friendly

 DESCRIPTION (provided by applicant): HyPhy (://www.hyphy.org) is a scriptable software platform designed to enable flexible and powerful analyses of DNA, RNA, codon, amino acid and other types of sequence data in an evolutionary context. Since their initial formal release in 2005, HyPhy and it's free web server Data Monkey (://www.datamonkey.org) have become stable and mature, cited in over 2,000 peer-reviewed publications, described in multiple book chapters, and been the subject of many invited workshops. In the first four-year funding cycle we focused on improvements and hardening of the "back end" elements of the HyPhy system. In this proposal, while we will still do work at that level, we focus more on the "front end" where interactions with users are key. Aim 1: Re-architect the HyPhy analytical engine and its scripting language 1.1 Redesign the HyPhy Batch Language (HBL) to enhance its productivity, reliability, maintain- ability, portability and reusability; this will be done while maintaining backward compatibility. 1.2 Redevelop the standard library of evolutionary models, standard analyses, and inference procedures to make them self-documenting, easy to learn, easy to extend, robust to inadvertent misapplication, and compliant with data exchange formats and communication protocols. Aim 2: Models and algorithms for large and complex datasets. 2.1 Improve HyPhy performance to handle much larger data sets in a single analysis by accelerating the fundamental operations in hardware and software. 2.2 Allow users to combine sequence and other quantitative data in a likelihood framework. 2.3 Develop a library of analyses for rapidly evolving pathogens and immune repertoires. Aim 3: Web browser based graphical interface for all computing devices. Presently, the majority of HyPhy users interact with the program through www.datamonkey.org. Keeping in mind the demand for such a user experience, we will: 3.1 Implement a complete interface for data exploration, analysis definition, job execution, and result interpretation and visualization as a local web application. This interface will run on computers, tables, and smartphones. 3.2 Develop the computational core of HyPhy as a native browser plug-in, making HyPhy an "app" distributed, maintained, and run entirely in a browser. 3.3 Re-implement datamonkey.org using modern web technologies (node.js); provide a public instance which can be accessed from any instance of HyPhy, and a distribution that can allow labs to set up their own cluster- or cloud-based instances.

 描述（由适用提供）：hyphy（：//www.hyphy.org）是一个可脚本的软件平台，旨在在进化环境中启用DNA，RNA，CORDON，氨基酸和其他类型的序列数据的灵活和强大的分析。自2005年最初的正式发布以来，Hyphy及其免费的Web服务器数据Monkey（：//www.datamonkey.org）已变得稳定且成熟，并在2,000多个同行评审的出版物中引用，在多个书籍章节中描述，并且是许多受邀研讨会的主题。在第一个四年的筹资周期中，我们着重于Hyphy系统的“后端”元素的改进和硬化。在此建议中，尽管我们仍将在该级别上工作，但我们将更多地关注“前端” 与用户的交互是关键。 AIM 1：重新构建Hyphy分析引擎及其脚本语言1.1重新设计Hyphy Batch语言（HBL），以提高其生产率，可靠性，可靠性，可移植性和可靠性；这将在保持向后兼容性的同时完成。 1.2重新开发了进化模型，标准分析和推理程序的标准库，以使其自我记录，易于学习，易于扩展，对无意间的错误应用以及符合数据交换格式和通信协议。 AIM 2：大型和复杂数据集的模型和算法。 2.1通过加速硬件和软件中的基本操作，在单个分析中提高Hyphy性能以处理更大的数据集。 2.2允许用户将序列和其他定量数据组合在可能性框架中。 2.3开发一个分析库，以快速发展的病原体和免疫曲目。 AIM 3：用于所有计算设备的基于Web浏览器的图形接口。目前，大多数Hephy用户通过www.datamonkey.org与该程序进行交互。考虑到对这种用户体验的需求，我们将：3.1实现一个完整的界面，以供数据探索，分析定义，作业执行以及结果解释和可视化作为本地Web应用程序。该界面将在计算机，表和智能手机上运行。 3.2将Hyphy的计算核心作为本机浏览器插件，使Hyphy成为分布，维护和完全在浏览器中运行的“应用”。 3.3使用现代Web Technologies（node.js）重新实现datamonkey.org;提供一个可以从Hyphy的任何实例访问的公共实例，以及可以允许实验室设置自己的群集或基于云的实例的分发。