Visualization software for genomics

基因组学可视化软件

• 批准号: 10428456
• 负责人: Ann E Loraine
• 金额: $ 35.97万
• 依托单位: UNIVERSITY OF NORTH CAROLINA CHARLOTTE
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-07-01 至 2026-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10428456
• 关键词: Algorithms; Big Data; Bioinformatics; Biological Assay; Biological Sciences; Charge; Clinical; Cloud Computing; Cognitive; Collaborations; Collection; Communities; Complex; Computer software; Computers; Data; Faculty; Genome; Genomics; Knowledge; Learning; Life; Methods; Pattern; Privatization; Public Sector; Research; Research Personnel; Resources; Scientist; Software Design; Software Tools; Students; Training Programs; Visual; Visual system structure; Visualization; Visualization software; analytical tool; cloud platform; cognitive system; computer science; cost; experimental study; genome browser; improved; innovation; large scale data; method development; novel; novel strategies; open source; programs; skills; software development; student training; tool; trend

To gain maximum benefit from big data in genomics, biologists need software tools that enhance our in- born cognitive and visual faculties. Our visual and cognitive systems possess extraordinary power to recognize patterns, and visual analytics software applications aim to enhance this ability by providing visual, interactive interfaces to data. My research focuses on developing visual analytics tools and associated resources for life scientists, using Integrated Genome Browser as a platform for delivery and experimentation. Integrated Genome Browser is a fast, highly customizable, freely available open source desktop genome browser application developed since the early 2000s that now serves thousands of users worldwide. By developing and supporting IGB for its thousands of users, my research contributes innovative new approaches for genome browsing that other visualization research programs can and do build upon. During the next five years, I will continue using state-of-the-art open source software development methods adapted to an academic setting to build and release advanced tools at low cost, while training students in computer science and bioinformatics. First, I will continue to develop new ways to exploit emerging public and private cloud infrastructure to meet biologists’ increasingly complex needs for advanced visual analytics. Using commercial and free-of-charge, public sector cloud platforms, my students and I will experiment with connecting Integrated Genome Browser to storage and visual analytics computing capability exceeding what is possible to achieve on a single, desktop computer. These advanced features within IGB will help move the entire field forward by demonstrating how application developers can harness the power of the cloud for visualizing data. Second, I will continue to build IGB and related tools into a platform that other developers can exploit and learn from. The field of genomics changes rapidly. As new methods and tools come on-line, developers need ways to create new visualization tools suited to these new methods. My research aims to provide a platform for experimentation that will enable developers in bioinformatics to build and release new visual analytics algorithms more rapidly to larger numbers of potential users. My group will continue to develop and support an App Store for IGB, an on-line clearinghouse for developers to distribute Apps and for users to find and install Apps relevant to their research. To support developers, we will continue to improve IGB’s internal application programmer’s interface (API), a collection of methods and classes crafted to enable developers of varying skill and knowledge to add new functions and features to the IGB interface. Third, my students and I will continue to explore larger concepts of community, open source software development, and humane software design by connecting tool builders with tool users to promote collaboration and innovation for the benefit of all.

为了从基因组学大数据中获得最大利益，生物学家需要能够增强我们的能力的软件工具。 与生俱来的认知和视觉能力。我们的视觉和认知系统拥有非凡的力量 识别模式，视觉分析软件应用程序旨在通过提供 数据的可视化、交互式界面。我的研究重点是开发可视化分析工具和 生命科学家的相关资源，使用集成基因组浏览器作为交付和 实验。集成基因组浏览器是一个快速、高度可定制、免费提供的开源软件 自 2000 年代初开发的桌面基因组浏览器应用程序，现已为数千人提供服务 全球用户。通过为数以千计的用户开发和支持 IGB，我的研究做出了贡献 其他可视化研究程序可以做到的基因组浏览创新方法 建立在。未来五年，我将继续使用最先进的开源软件 适应学术环境的开发方法，以低成本构建和发布先进的工具， 同时培训学生计算机科学和生物信息学。第一，我会不断开发新的方式 利用新兴的公共和私有云基础设施来满足生物学家日益复杂的需求 用于高级可视化分析。使用商业和免费的公共部门云平台，我的 我和学生将尝试将集成基因组浏览器连接到存储和视觉 分析计算能力超出了单个台式计算机所能实现的能力。 IGB 中的这些高级功能将通过展示如何帮助推动整个领域向前发展 应用程序开发人员可以利用云的力量来可视化数据。第二，我会继续 将 IGB 和相关工具构建成其他开发人员可以利用和学习的平台。领域 基因组学变化很快。随着新方法和工具的出现，开发人员需要方法来创建 适合这些新方法的新可视化工具。我的研究旨在提供一个平台 实验将使生物信息学开发人员能够构建和发布新的可视化分析 算法更快地传播给更多的潜在用户。我的团队将不断发展壮大 支持 IGB 的应用程序商店，这是一个供开发人员分发应用程序以及供用户分发应用程序的在线交换所 查找并安装与其研究相关的应用程序。为了支持开发者，我们将继续改进 IGB 内部应用程序程序员接口 (API)，是精心设计的方法和类的集合 具有不同技能和知识的开发人员可以向 IGB 接口添加新的功能和特性。第三， 我和我的学生将继续探索社区、开源软件的更大概念 通过将工具构建者与工具用户联系起来以促进开发和人性化软件设计 协作和创新，造福所有人。