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（由申请人提供）：HyPhy (://www.hyphy.org) 是一个可编写脚本的软件平台，旨在实现在进化背景下对 DNA、RNA、密码子、氨基酸和其他类型的序列数据进行灵活而强大的分析。自 2005 年首次正式发布以来，HyPhy 及其免费网络服务器 Data Monkey (://www.datamonkey.org) 已经变得稳定和成熟，在 2,000 多种同行评审出版物中被引用，在多本书章节中进行了描述，并成为许多受邀研讨会的主题。在第一个四年资助周期中，我们专注于 HyPhy 系统“后端”元素的改进和强化。在这个提案中，虽然我们仍然会在这个层面上做工作，但我们更多地关注“前端”，其中 与用户的互动是关键。目标1：重新架构HyPhy分析引擎及其脚本语言 1.1重新设计HyPhy批处理语言（HBL），以提高其生产力、可靠性、可维护性、可移植性和可重用性；这将在保持向后兼容性的同时完成。 1.2 重新开发进化模型、标准分析和推理程序的标准库，使其具有自记录性、易于学习、易于扩展、对无意误用具有鲁棒性，并符合数据交换格式和通信协议。目标 2：大型复杂数据集的模型和算法。 2.1 通过加速硬件和软件的基本操作，提高 HyPhy 性能，以便在单次分析中处理更大的数据集。 2.2 允许用户在可能性框架中组合序列和其他定量数据。 2.3 开发快速进化的病原体和免疫库的分析库。目标 3：适用于所有计算设备的基于 Web 浏览器的图形界面。目前，大多数 HyPhy 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 作为本地 Web 应用程序实现数据探索、分析定义、作业执行以及结果解释和可视化的完整界面。该界面将在计算机、平板电脑和智能手机上运行。 3.2 将HyPhy的计算核心开发为原生浏览器插件，使HyPhy成为完全在浏览器中分布式、维护和运行的“应用程序”。 3.3 使用现代网络技术（node.js）重新实现 datamonkey.org；提供可从任何 HyPhy 实例访问的公共实例，以及允许实验室设置自己的集群或基于云的实例的发行版。