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Integrated Genome Browser and IGB Apps

集成基因组浏览器和 IGB 应用程序

基本信息

批准号：
9767771
负责人：
Ann E Loraine
金额：
$ 37.21万
依托单位：
UNIVERSITY OF NORTH CAROLINA CHARLOTTE
依托单位国家：
美国
项目类别：
财政年份：
2011
资助国家：
美国
起止时间：
2011-07-01 至 2021-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9767771
关键词：
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 Scientist 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 analysis pipeline application programming interface base cloud based cloud storage computerized data processing data integration data sharing design flexibility genome browser genome-wide genomic data graphical user interface improved innovation insight member novel social media software development tool usability user friendly software user-friendly

项目摘要

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.

项目摘要生物医学研究越来越多地涉及对大量数据集的检查。新的高度介绍- 通量测序技术已经导致了几十个新的基因组序列的产生，并促使人们做出重大努力，对人类个体基因组进行测序。采取为了充分利用这些新的大规模数据集，研究人员需要灵活、用户友好的一种支持交互式深入探索不同详细级别数据的软件，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技术旨在帮助科学家探索基因组规模的数据集，最终导致更好的随着科学家使用IGB来更深入地了解基因和基因组，本项目将继续开发IGB软件，增加新的数据集成和显示用户所要求的功能，IGB开发人员预计将越来越多地面对基因组学正在进行的快速技术变革，这一点非常重要。重大改进将包括将IGB图形用户界面迁移到JavaFX，JavaFX是作为Java的一部分发布的工具包 8，取代了Swing工具包;速度和内存的改进，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用从数据中推断出的新特征来注释基因组场景; 交互式可变剪接可视化。该项目将开发和强化综合基因组浏览器应用程序编程接口（API），用于开发人员，将IGB转换为灵活易用的框架，用于构建和分发全新的可视化作为IGB应用程序，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，我们将利用社交媒体、在线培训和面对面培训，加快用户培训和推广研讨会，帮助研究人员通过以下方式深入了解生物信息学分析视觉化该项目将扩大IGB用户社区，其中包括与数据，程序员寻求建立强大的新工具，生物信息学分析师寻求简单的将可视化纳入数据分析管道的方法。