Integrated Genome Browser and IGB Apps

集成基因组浏览器和 IGB 应用程序

• 批准号: 9175578
• 负责人: Ann E Loraine
• 金额: $ 37.39万
• 依托单位: UNIVERSITY OF NORTH CAROLINA CHARLOTTE
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-07-01 至 2020-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9175578
• 关键词: Accounting; Alternative Splicing; Animals; Architecture; Base Pairing; Big Data; Bioinformatics; Biological Sciences; Biomedical Research; Chromosomes; Code; Communities; Computer Systems; Computer software; Computers; Data; Data Analyses; Data Display; Data Files; Data Science; Data Set; Data Storage and Retrieval; Development; Disease; Disease susceptibility; Education and Outreach; Educational workshop; Environment; Genes; Genome; Genomic Library; Genomics; Genotype; Health; Health Professional; High-Throughput Nucleotide Sequencing; Human; Human Genome; Imagery; Individual; Java; Laboratories; Language; Lead; Link; Memory; Methods; Outcome; Performance; Persons; Plants; Play; Production; Programming Languages; Public Health; Recording of previous events; Research Personnel; Resources; Role; Scientist; Services; Source; Speed; Students; Surveys; System; Techniques; Technology; Time; Training; Update; Visual; Visualization software; Work; application programming interface; base; cloud based; computerized data processing; data integration; data sharing; data visualization; design; flexibility; genome browser; genome sequencing; genome-wide; graphical user interface; improved; innovation; insight; member; novel; programs; social media; software development; tool; usability; user friendly software; user-friendly

Project Summary Biomedical research increasingly involves examination of huge data sets. Introduction of new high- throughput sequencing technologies has led to production of new genome sequence for dozens of plants and animals and prompted major efforts to sequence individual human genomes. To take full advantage of these new large-scale data sets, researchers require flexible, user-friendly software that supports interactive, in-depth exploration of data at different levels of detail, ranging from chromosomes to individual base pairs. The Integrated Genome Browser (IGB) is a desktop, java-based genome browser implemented that implements innovative yet practical visualization techniques designed to help scientists explore genome-scale data sets, ultimately leading to better treatments for disease as scientists use IGB to achieve deeper insight into genes and genomes. This project will continue to develop the IGB software, adding new data integration and display features users have requested and which the IGB developers foresee will become increasingly important in the face of on-going and rapid technological change in genomics. Major improvements will include migrating the IGB graphical user interface to JavaFX, a toolkit released as part of Java 8 that replaces the Swing toolkit; speed and memory improvements for interactive display of large datasets; integration with cloud-based data storage resources; an all-new editing capability enabling users to annotate genomic scenes with new features inferred from data; and a new interactive alternative splicing visualization. The project will develop and harden the Integrated Genome Browser Application Programming Interface (API) for developers, transforming IGB into a flexible and easy-to-use framework for building and distributing all-new visualizations as IGB Apps, OSGi plug-ins that users will access via a new IGB App Store. To maximize project impact, we will accelerate user training and outreach, using social media, on-line training, and in-person workshops to help researchers develop deeper insight into bioinformatics analysis through visualization. This project will grow the IGB user community, which includes scientists working with data, programmers seeking to build powerful new tools, and bioinformatics analysts seeking easy ways to incorporate visualization into data analysis pipelines.

项目概要 生物医学研究越来越多地涉及对庞大数据集的检查。引进新高 高通量测序技术已导致数十种新基因组序列的产生 植物和动物，并推动了对人类个体基因组测序的重大努力。采取 充分利用这些新的大规模数据集，研究人员需要灵活、用户友好的 支持交互式、深入探索不同细节级别的数据的软件 从染色体到单个碱基对。集成基因组浏览器（IGB）是一个桌面， 基于java的基因组浏览器实现了创新而实用的可视化 旨在帮助科学家探索基因组规模数据集的技术，最终带来更好的结果 科学家使用 IGB 来更深入地了解基因和基因组，从而治疗疾病。 该项目将继续开发IGB软件，增加新的数据集成和显示 用户要求的功能，IGB 开发人员预计这些功能将变得越来越多 面对基因组学持续快速的技术变革，这一点非常重要。主要改进 将包括将 IGB 图形用户界面迁移到 JavaFX，这是作为 Java 一部分发布的工具包 8 取代了 Swing 工具包；大型交互式显示的速度和内存改进 数据集；与基于云的数据存储资源集成；全新的编辑功能 使用户能够使用从数据推断出的新特征来注释基因组场景；和一个新的 交互式选择性剪接可视化。该项目将开发和强化集成 为开发人员提供的基因组浏览器应用程序编程接口 (API)，将 IGB 转变为 灵活且易于使用的框架，用于构建和分发全新可视化作为 IGB 应用程序， 用户将通过新的 IGB App Store 访问 OSGi 插件。为了最大限度地提高项目影响力，我们将 利用社交媒体、在线培训和面对面的方式加速用户培训和推广 研讨会帮助研究人员通过以下方式更深入地了解生物信息学分析 可视化。该项目将扩大 IGB 用户社区，其中包括与 数据、寻求构建强大新工具的程序员以及寻求简单的生物信息学分析师 将可视化纳入数据分析流程的方法。