Integrated Genome Browser and IGB Apps

项目摘要 生物医学研究越来越多地涉及对庞大数据集的检查。介绍了新一代高科技产品 吞吐量测序技术已经导致了数十种新基因组序列的产生 植物和动物，并推动了对单个人类基因组测序的重大努力。去拿 充分利用这些新的大规模数据集，研究人员需要灵活、人性化的 支持在不同细节级别、范围内对数据进行交互式深入研究的软件 从染色体到单个碱基对。集成基因组浏览器(IGB)是一个桌面， 实现了基于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，最终导致更好的 疾病的治疗，因为科学家使用IGB来更深入地了解基因和基因组。 该项目将继续开发IGB软件，增加新的数据集成和显示 用户已请求且IGB开发人员预计将越来越多的功能 在面对基因组学持续和快速的技术变革时，这一点很重要。重大改进 将包括将IGB图形用户界面迁移到作为Java一部分发布的工具包JavaFX 8，它取代了Swing工具包；速度和内存方面的改进可用于交互显示大型 数据集；与基于云的数据存储资源集成；全新的编辑功能 使用户能够用从数据推断出的新特征来注释基因组场景；以及新的 交互式选择性剪接可视化。该项目将发展和强化一体化的 面向开发人员的基因组浏览器应用编程接口(API)，将IGB转换为 灵活且易于使用的框架，用于构建和分发以IGB应用程序形式的全新可视化效果， 用户将通过新的IGB应用商店访问的OSGi插件。为了最大限度地发挥项目的影响，我们将 使用社交媒体、在线培训和面对面培训，加快用户培训和推广 帮助研究人员更深入地了解生物信息学分析的工作坊 视觉化。该项目将扩大IGB用户社区，其中包括与以下项目合作的科学家 数据，程序员寻求建立强大的新工具，以及生物信息学分析师寻求轻松 将可视化整合到数据分析管道中的方法。

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.