The Integrative Genomics Viewer (IGV) for Cancer Research

用于癌症研究的综合基因组学查看器 (IGV)

• 批准号: 10483114
• 负责人: JILL P. MESIROV
• 金额: $ 87.17万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-07 至 2026-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10483114
• 关键词: Address; Architecture; Bioinformatics; Clinic; Clinical; Code; Collaborations; Communities; Complex; Computer software; Data; Development; Disease; Documentation; Electronic Mail; Elements; Emerging Technologies; Ensure; Environment; Event; Evolution; Exercise; Future; Generations; Genomics; Goals; Java; Letters; Libraries; Link; Malignant Neoplasms; Methods; Nucleotides; Operating System; Patients; Performance; Publications; Reporting; Research; Research Personnel; Resources; Software Engineering; Software Tools; Suggestion; Technology; Time; Training; Treatment Protocols; Update; Validation; Variant; Visualization; Walking; Work; anticancer research; base; cancer genomics; cancer therapy; clinical sequencing; cloud based; computerized data processing; data acquisition; data visualization; experience; family support; flexibility; genomic data; genomic tools; improved; insight; interoperability; light weight; new technology; new therapeutic target; novel; open source; precision oncology; programs; research study; response; success; tool; tumor; usability; user-friendly; web app

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 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, and released in 2008, a broadly applicable Integrative Genomics Viewer (IGV). IGV is an interactive, high-performance, user-friendly tool launched millions of times a year by investigators and clinicians worldwide. 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. Aim 1. Evolve IGV to keep pace with the needs of the cancer genomics community. We will continue to evolve IGV to leverage recent and future advances in genomics technologies and methods that are key to moving cancer research and treatment forward. We will add new visualizations and features to better enable interpretation and validation of complex variants from both short and long read data. Through collaborations with other projects we will add new capabilities to better assess and interpret single nucleotide and structural variants. Responding to IGV’s increased use for review of variants in patient tumors, we will enhance support for this task. Aim 2. Maintain IGV to ensure continued high levels of utility, usability, and reliability. We will continue to provide frequent software releases to address feature requests, bug reports, and other suggestions from IGV’s community of both users and developers. Based on community input, we will review the IGV user interface to improve usability. We will address the challenges and opportunities presented by the evolving computing and software technology environment. We will continue to maintain the code base and downloadable installers and update them for new releases of Java, JavaScript, external libraries, browsers, and operating systems. Aim 3. Support the IGV user and open-source developer communities. We will continue to provide a high level of support including rapid responses to help requests; in-depth documentation on software use; short videos to walk users through tasks with high utility; training materials and exercises. For our vibrant, open-source developer community that contributes to the IGV code base and uses IGV in their own applications or resources, support includes: documentation and code examples for integrating and extending IGV; guidance on new development through our GitHub forums; prompt review of contributions; and acknowledgement of their work. We have extensive software engineering experience, developing and distributing IGV and other software tools used by hundreds of thousands of biomedical researchers and clinicians worldwide. IGV’s success, user-driven development approach, collaborative tradition, and flexible architecture make us well poised to accomplish our aims to further transform data visualization and accelerate the pace of biomedical discovery.

项目摘要/摘要 在新的和新兴的数据获取技术的驱动下，综合基因组研究正在革新 我们处理癌症研究并绘制新治疗方案的方式的方式。他们需要 高通量生成和分析多种且通常是复杂的基因组数据类型。解决这个问题 挑战，以及与最终用户的积极合作，我们于2008年开发并发行了广泛适用的 综合基因组观察者（IGV）。 IGV是一种交互式，高性能，用户友好的工具，启动了数百万美元 全球调查人员和临床医生每年每年。该项目的目的是确保IGV继续进行。 跟踪和响应基因组技术和不断变化的用户需求的进步，并保持其高水平 癌症研究界的实用程序。我们将通过我们的三个特定目标来实现这一目标。 目标1。进化IgV，以使空间满足癌症基因组学界的需求。我们将继续 进化IGV利用基因组技术和方法的最新进步，这是移动的关键 癌症研究和治疗前进。我们将添加新的可视化和功能以更好地启用 简短和长阅读数据的复杂变体的解释和验证。通过与之合作 其他项目，我们将添加新的功能，以更好地评估和解释单核苷酸和结构变体。 为了响应IGV对患者肿瘤中变体的审查的增加，我们将增强对这项任务的支持。 目标2。维护IGV，以确保持续的高度效用，可用性和可靠性。我们将继续 经常提供软件发行以解决功能请求，错误报告和IGV的其他建议 用户和开发人员的社区。根据社区的输入，我们将查看IGV用户界面 提高可用性。我们将解决不断发展的计算和机遇的挑战和机遇 软件技术环境。我们将继续维护代码库和可下载的安装程序以及 将它们更新以获取Java，JavaScript，外部库，浏览器和操作系统的新版本。 目标3。支持IGV用户和开源开发人员社区。我们将继续提供高 支持水平，包括快速响应以帮助请求；有关软件使用的深入文档；简短的视频 引导用户完成高实用程序的任务；培训材料和练习。对于我们充满活力的开源 为IGV代码基础做出贡献并在其自己的应用程序或资源中使用IGV的开发人员社区， 支持包括：用于集成和扩展IGV的文档和代码示例；新指南 通过我们的GitHub论坛发展；及时审查贡献；并承认他们的工作。 我们拥有丰富的软件工程经验，开发和分发IGV和其他软件工具 全球数十万生物医学研究人员和临床医生使用。 IGV的成功，用户驱动 开发方法，协作传统和灵活的建筑使我们有毒化的毒品 旨在进一步改变数据可视化并加速生物医学发现的空间。