The Integrative Genomics Viewer (IGV): visualization supporting cancer research

项目摘要/摘要 在新的和新兴的数据获取技术的推动下，综合基因组研究正在带来革命性的变化 我们研究癌症和其他疾病的方式，以及绘制新治疗方法的道路 养生法。它们需要以高吞吐量生成和分析多种类型的，而且通常是复杂的 基因组数据。为了应对这一挑战，并与最终用户积极合作，我们开发了一种广泛的 适用的整合基因组学查看器(IGV)。IGV是一款高性能、用户友好的工具，由超过 全球100,000名研究人员和临床医生，以交互方式探索大型整合基因组 数据集。该项目的目标是确保免疫球蛋白继续跟踪和应对基因组学方面的进展 技术和不断变化的用户需求，并保持其对癌症研究社区的高水平实用。 我们将通过下面描述的三个具体目标来实现这一目标。 目标1.确保IGV继续跟上新技术和新兴技术的步伐 改变癌症研究环境，我们将开发新的和改进的IGV观点，例如，远程 基因组事件、物理接近数据等。为了认识到生物医学社区的不断增长 使用云，我们将确保高效且可访问的云数据可视化和无缝集成 使用分析工作流。IGV咨询委员会将确保我们拥有最好的跟踪技术和用户需求。 目标2.为了增强、改进和维护免疫球蛋白，以便最好地支持癌症研究人员的工作，我们将 根据IGV用户社区的反馈和建议开发新功能和更新。我们会 也利用对癌症研究和发展有价值的外部资源 支持在自己的应用程序和资源中使用IGV的其他项目。我们将特别注意 在用于癌症研究的信息学技术(ITCR)工具系列中的协作和倡议。 目标3.为癌症研究社区提供培训、支持和推广活动，我们将 继续提供我们的电子邮件帮助台、研讨会和文档以帮助用户和开发人员 社区最大限度地利用免疫球蛋白。重要的是，我们将开发一种新的聚焦IGV集合 “草图”，引导用户完成可视化任务，具有很高的实用性。 我们在软件工程方面拥有丰富的经验，包括IGV和 世界各地数十万生物医学研究人员和临床医生使用的其他软件工具。我们 将继续我们的用户驱动的开发方法，与大型基因组学项目密切合作 癌症基因组图谱，NCI支持的软件项目，如癌症基因组学云试点和ITCR 计划，以及许多单一调查者研究。IGV目前的成功、灵活的架构和我们的 支持外部发展的计划使我们做好准备，实现进一步转变数据的目标 可视化，加快生物医学发现的步伐。

Project Summary/Abstract Driven by new and emerging technologies for data acquisition, integrative genomic studies are revolutionizing the way we approach the study of cancer and other diseases, and charting the way to novel treatment regimens. They require the high-throughput generation and analysis of multiple, and often complex, types of genomic data. To address this challenge, and in active collaboration with end users, we developed a broadly applicable Integrative Genomics Viewer (IGV). IGV is a high-performance, user-friendly tool used by over 100,000 investigators and clinicians worldwide for the interactive exploration of large, integrated genomic datasets. The goal of this project is to ensure that IGV continues to track and respond to advances in genomics technology and changing user needs, and maintains its high level of utility for the cancer research community. We will accomplish this through our three specific aims as described below. Aim 1. To ensure that the IGV continues to keep pace with new and emerging technologies and the changing cancer research environment we will develop new and improved IGV views of, e.g., long range genomic events, physical proximity data, and more. In recognition of the biomedical community's increasing use of the cloud, we will ensure efficient and accessible visualization of cloud data and seamless integration with analysis workflows. An IGV Advisory Board will ensure we are best tracking technologies and user needs. Aim 2. To enhance, refine, and maintain IGV to best support cancer researchers in their work we will develop new features and updates based on feedback and suggestions from the IGV user community. We will also take advantage of external resources that are valuable for cancer research, as well as development in support of other projects that use IGV in their own applications and resources. Special attention will be paid to collaborations and initiatives within the Informatics Technology for Cancer Research (ITCR) family of tools. Aim 3. To provide training, support, and outreach activities for the cancer research community we will continue to provide our email help desk, workshops and documentation to help both the user and developer communities take best advantage of IGV. Importantly, we will develop a new collection of focused IGV “sketches” to walk users through visualization tasks with high utility. We have extensive experience in software engineering, including the development and distribution of IGV and other software tools used by hundreds of thousands of biomedical researchers and clinicians worldwide. We will continue our user-driven development approach working closely with large genomics projects like The Cancer Genome Atlas, NCI supported software projects like the Cancer Genomics Cloud Pilots and the ITCR program, as well as numerous single-investigator studies. IGV's current success, flexible architecture, and our plan to support external development make us well poised to accomplish our aims to further transform data visualization and accelerate the pace of biomedical discovery.