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

 描述(申请人提供)：对于许多生物医学研究人员来说，大数据时代既令人兴奋又充满挑战--令人兴奋是因为科学和医学上的可能性，而挑战是因为他们缺乏信息技术(IT)背景。随着DNA测序成本的持续下降，许多研究人员希望通过芯片序列和RNA-序列技术等对新的基因组进行测序和分析，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分析和可视化，以分析和注释真核基因组。该项目将开发集成软件，使任何研究人员能够构建具有来自多种分析工具的证据跟踪的基因组浏览器，使用浏览器以交互方式注释基因组的功能元件。通过在本科教育中使用该系统，将扩大项目的利用率。基因组注释项目已被证明为将生物信息学纳入本科课程和让本科生参与研究提供了一个极好的工具。一旦他们经历了一些成功，并看到并欣赏了这样一个系统的力量，生物医学研究人员和本科生可能都会有动力学习更多的IT技能。方法：该项目是Galaxy Project和GEP之间的合作伙伴关系。Galaxy Project是一个基于网络的工作台，它提供了一大套生物信息学工具和共享的工作流程，GEP由来自100所本科院校的教师组成，他们在向学生介绍基因组学方面拥有丰富的经验。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，该管道将促进基因组注释，使现有和新基因组(例如寄生虫)的众多分布式项目成为可能。该系统将使生物医学研究人员和教职员工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社区都受益。G-onramp的Beta测试将由GEP的教职员工和其他早期采用者进行。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GEP和Galaxy之间的广泛对话来完成。最终的系统将对新手来说是可访问的，对专家来说是有用的。目标3将重点放在传播上。这将通过基于网络的公告、简短的会议研讨会和较长的“培训培训师”研讨会来实现；通过GEP推出该系统将提供100个校园和1000个本科生的起步池。提供广泛的基因组分析和注释系统将大大加强生物信息学研究和生物医学部门的培训，使基础和应用研究都将有助于 NHGRI的“从碱基对到床边”的宪章。

 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.