A Genome Browser On-Ramp to Engage Biologists with Big Data

 描述（由申请人提供）：“大数据”时代对许多生物医学研究人员来说既令人兴奋又具有挑战性-令人兴奋的是科学和医学的可能性，而具有挑战性的是他们缺乏信息技术（IT）背景。随着DNA测序成本的不断下降，许多研究人员希望通过ChIP-seq和RNA-seq技术等来测序和分析新的基因组，并建立基因组功能的知识，但发现自己受到IT需求的限制。我们的目标是创建一个可广泛访问的基于Web的应用程序（命名为G-OnRamp），用于基因组数据的交互式分析和可视化，以分析和注释真核生物基因组。该项目将开发集成软件，使任何研究人员都能够使用来自多种分析工具的证据跟踪构建基因组浏览器，使用浏览器交互式注释基因组的功能元素。在本科教育中使用该系统将扩大项目利用率。基因组注释项目已被证明提供了一个了不起的车辆，将生物信息学纳入本科课程，并从事研究的本科生。一旦他们取得了一些成功，并看到并欣赏到这样一个系统的力量，生物医学研究人员和本科生都可能会有动力学习更多的IT技能。方法：该项目是银河项目和基因组学教育合作伙伴关系（GEP）之间的合作，银河项目是一个基于网络的工作台，提供了大量的生物信息学工具和共享工作流程，基因组学教育合作伙伴关系（GEP）由来自100多个主要本科院校的教师组成，在向学生介绍基因组学方面具有广泛的经验。目标1：生物学家和计算机科学家之间的合作努力，为基因组学分析创建更好的管道，并将它们与基因组浏览器构建管道集成，这将促进基因组注释，使现有和新基因组的许多分布式项目成为可能（例如，寄生虫）。该系统将使生物医学研究人员和教师能够建立新的本地项目;将用户链接到所需的网络资源;并为协作注释项目提供一种手段。众包基因组注释将使学生和生物医学研究界受益。G-OnRamp的Beta测试将由GEP教师和其他早期采用者完成。目标2：为初学者和专家编写关于使用该系统的培训材料。这将通过两性平等方案与银河系统之间的广泛对话来实现。最终的系统将是一个新手访问，和有用的专家。目标3将侧重于传播。这将通过网上公告、短期会议讲习班和较长的“培训培训员”讲习班来实现;通过两性平等观点方案引入该系统将提供一个超过100个校园和超过1 000名本科生的初始人才库。提供广泛使用基因组分析和注释系统的机会将大大加强生物医学部门的生物信息学研究和培训，使基础和应用研究都能作出贡献， NHGRI的“从碱基对到床边”宪章。

 DESCRIPTION (provided by applicant): The era of "big data" is both exciting and challenging for many biomedical investigators - exciting because of the scientific and medical possibilities, and challenging because of their lack of background in information technology (IT). As DNA sequencing costs continue to drop, many investigators would like to sequence and analyze new genomes as well as build knowledge of genome function through ChIP-seq and RNA-seq technologies, etc., but find themselves limited by the IT demands. Our goal here is to create a widely-accessible Web-based application (christened G-OnRamp) for interactive analysis and visualization of genomic data to analyze and annotate eukaryotic genomes. This project will develop integrated software that will enable any investigator to construct genome browsers with evidence tracks from multiple analysis tools, using the browser to interactively annotate the functional elements of a genome. Project utilization will be amplified by the use of the system in undergraduate education. Genome annotation projects have been shown to provide a terrific vehicle both for bringing bioinformatics into the undergraduate curriculum, and for engaging undergraduates in research. Once they experience some success, and see and appreciate the power of such a system, both biomedical researchers and undergraduates alike may be motivated to learn additional IT skills. Approach: the project is a partnership between the Galaxy Project, a web-based workbench that provides access to a large suite of bioinformatics tools and shared workflows, and the Genomics Education Partnership (GEP), made up of faculty from >100 primarily undergraduate institutions, with broad experience in introducing students to genomics. Aim 1: a collaborative effort between biologists and computer scientists to create better pipelines for genomics analysis, and integrate them with a genome browser construction pipeline that will facilitate genome annotation, enabling numerous distributed projects for both existing and novel genomes (e.g., a parasite). The system will enable biomedical researchers and faculty to set up new, local projects; link users to the needed web resources; and provide a means for collaborative annotation projects. Crowd-sourcing genome annotation will benefit both students and the biomedical research community. Beta-testing of G-OnRamp will be done by GEP faculty and other early adopters. Aim 2: develop training materials on the use of the system for both beginners and experts. This will be done with extensive dialogue between GEP and Galaxy. The final system will be accessible for a novice, and useful for an expert. Aim 3 will focus on dissemination. This will be done through Web-based announcements, short meeting workshops and longer "train the trainer" workshops; introducing the system through the GEP will provide a starting pool of >100 campuses and >1000 undergraduates. Providing broad access to a system for genome analysis and annotation will greatly strengthen bioinformatics research and training in the biomedical sector, enabling both basic and applied studies that will contribute to NHGRI's "base pairs to bedside" charter.