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)

基本信息

批准号：
10704678
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
项目类别：
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/10704678
关键词：
Acceleration 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 Training Treatment Protocols Update Validation Variant Visual 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 genome resource 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

项目摘要

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.

项目概要/摘要在新兴数据采集技术的推动下，综合基因组研究正在发生革命性的变化我们研究癌症的方式并制定新的治疗方案，他们需要多种且通常复杂类型的基因组数据的高通量生成和分析可以解决这个问题。挑战，并与最终用户积极合作，我们开发并于 2008 年发布了一个广泛适用的综合基因组查看器 (IGV) 是一款交互式、高性能、用户友好的工具，已推出数百万次。该项目的目标是确保 IGV 继续下去。跟踪和响应基因组学技术的进步和不断变化的用户需求，并保持其高水平我们将通过我们的三个具体目标来实现这一目标。目标 1. 不断发展 IGV，以满足癌症基因组学界的需求。发展 IGV，以利用基因组学技术和方法的最新和未来进步，这些技术和方法对于移动至关重要我们将添加新的可视化和功能以更好地促进癌症研究和治疗。通过与短读和长读数据的合作来解释和验证复杂的变体。在其他项目中，我们将添加新功能，以更好地评估和解释单核苷酸和结构变异。为了响应 IGV 越来越多地用于审查患者肿瘤变异的情况，我们将加强对这项任务的支持。目标 2. 维护 IGV 以确保持续高水平的实用性、可用性和可靠性。提供频繁的软件版本来解决 IGV 的功能请求、错误报告和其他建议用户和开发者社区根据社区意见，我们将审查 IGV 用户界面我们将应对不断发展的计算和技术带来的挑战和机遇。我们将继续维护代码库和可下载的安装程序。更新它们以适应新版本的 Java、JavaScript、外部库、浏览器和操作系统。目标 3. 支持 IGV 用户和开源开发者社区我们将继续提供高水平的服务。支持程度，包括对帮助请求的快速响应；有关软件使用的深入文档短视频；引导用户完成具有高实用性的培训材料和练习；为 IGV 代码库做出贡献并在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 新指南的文档和代码示例；通过我们的 GitHub 论坛进行开发；及时审查贡献并认可他们的工作。我们拥有丰富的软件工程经验，开发和分发 IGV 及其他软件工具 IGV 的成功源于用户驱动，被全球数十万生物医学研究人员和信徒所使用。开发方法、协作传统和灵活的架构使我们做好了完成我们的任务的准备旨在进一步转变数据可视化并加快生物医学发现的步伐。