A lightweight genome browser for data integration, exploration and interactive figures

用于数据集成、探索和交互式图形的轻量级基因组浏览器

• 批准号: BB/K015427/1
• 负责人: Tim Hubbard
• 金额: $ 10.83万
• 依托单位: Wellcome Sanger Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2013
• 资助国家: 英国
• 起止时间: 2013 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FK015427%2F1
• 关键词: lightweight; genome; browser; data; integration

Genome browsers are important tools for visualising, interpreting, andunderstanding the wealth of information now available about genomestructure, its functions, and the variations that occur betweenindividuals. In research environments, they are frequently used forvisually checking the quality of new data, looking for patterns andcorrelations, and inspecting the results of analysis tools. Browsersare also important for education, and -- especially with the arrival ofdirect-to-consumer genetic testing -- may also be of interest to thegeneral public.Historically, the most commonly-used genome browsers have been relativelystatic web applications, displaying a portion of the genome as a singleimage which must be reloaded to move or zoom the view, leaving majorbarriers to interactivity. The alternative is heavy-client desktopsoftware which is more interactive but requires installation. Dalliancetakes advantage of newer features of web browsers to build a fullyinteractive genome browsing tool as a web application.Because Dalliance does all the data integration and drawing work in codethat runs within the end users' web browsers, it is relativelystraightforward to add an instance to a new web page without anyserver-side work. The Dalliance instance can potentially be just one ofmany elements on a complex web page. This leads to the possibility ofcreating many kinds of applications which combine spatial views ofgenomic data with other information. We are already seeing a number ofcases where academic and industrial researchers have used Dalliance as abrowser component of their website, including the interpretation of DTCgenetic tests (see letters of support). You can even think of Dallianceas allowing the creation of interactive figures, which can accompanydatabase records, analysis results, or publications.We propose a program of further development work, rewriting the mainrendering code to improve performance, and splitting the user interfaceinto components. This means embedders have the flexibility to offereither a simplified interface (e.g. more appropriate to an interactivefigure), a fully-featured interface with a complete set of navigationcontrols tools to control the integration of additional datasets, oranything in between.We will add support for additional genomic data formats -- notably,better support for genetic variation data. We will also update themetadata model, and support additional metadata sources such as the"track hub" structures used by the UCSC browser. This will enable easyintegration of existing data from the ENCODE project, and offer a simpleroute for sharing biological datasets with enough metadata to allowdisplay in a genome browser with descriptions and track selection userinterfaces.Finally, we plan to organise a federated data workshop to interact withdevelopers and encourage the development of federated solutions for sharingbiological data. This will be modelled on the popular DAS workshop thathas been organised at Hinxton in the past, but with a broader aim ofsupporting and encouraging data integration in a variety of formats,notably the modern style of indexed binary data and trackhub-stylemetadata which allows discoverable data to be published with extremelylow requirements for server hardware or administration.

基因组浏览器是可视化，解释和理解目前可用的有关基因造影，其功能以及个人之间发生变化的大量信息的重要工具。在研究环境中，它们经常被发现使用，以检查新数据的质量，寻找模式和相关以及检查分析工具的结果。浏览器对教育也很重要，尤其是 - 尤其是直接到消费者的基因检测 - 总体上也可能引起人们的关注。历史上，最常用的基因组浏览器是相对较为久的网络应用程序，这是一部分基因组作为单一图像的一部分，必须重新添加或放置大型次数，以使大型次数互动。替代方案是重晶型桌面软件，它更具交互性，但需要安装。 DallianCetakes的优势是Web浏览器的较新功能，可以将完全相互作用的基因组浏览工具构建为Web应用程序。由于Dalliance在最终用户的Web浏览器中进行了所有数据集成和绘制工作，因此在最终用户的Web浏览器中运行，相对较差的是，将实例添加到无需任何工作的新网页中。 Dalliance实例可能只是复杂网页上的一个元素之一。这导致了创建多种应用程序的可能性，这些应用程序将基因组数据的空间视图与其他信息结合在一起。我们已经看到了许多案例，学术和工业研究人员将Dalliance用作其网站的删节部分，包括对DTCGENETIC测试的解释（请参阅支持信）。您甚至可以想到达利安卡斯（Dallianceas）允许创建交互式数字，这些图形可以伴随记录，分析结果或出版物。我们提出了一项进一步开发工作的程序，重写了Mainrendering Code以提高性能，以提高性能并拆分用户界面组件。这意味着嵌入式具有灵活性，可以灵活地使用简化的接口（例如，更适合于InteractiveFigure），这是一个完整的接口，具有完整的NavigationControls工具以控制其他数据集的集成，我们将在介于两者之间的集成。我们将添加支持其他基因组数据格式的支持，以更好地支持遗传数据，以更好地支持遗传数据。我们还将更新themetadata模型，并支持其他元数据源，例如UCSC浏览器使用的“轨道集线器”结构。这将使从编码项目中的现有数据轻松整合，并提供了一种简单的信息，可以与足够的元数据共享生物数据集，以允许在具有描述的基因组浏览器中允许display进行描述和跟踪选择UserInterfaces。我们计划组织一个联合数据研讨会，以与Federated federated Data Incorsing federated Dataiced一起组织联合数据工作室，以相互互动，并提供了共享的数据。这将以过去在Hinxton组织的流行DAS研讨会为基础，但具有更广泛的目标，以各种格式进行支持和鼓励数据集成，尤其是索引二进制数据的现代风格和TrackHub-Stylemetadata的现代风格，可发现可发现的数据及其针对服务器硬件或管理的极其损失。

项目成果

An interactive genome browser of association results from the UK10K cohorts project.

• DOI: 10.1093/bioinformatics/btv491
• 发表时间: 2015-12-15
• 期刊: Bioinformatics (Oxford, England)
• 作者: Geihs M;Yan Y;Walter K;Huang J;Memari Y;Min JL;Mead D;UK10K Consortium;Hubbard TJ;Timpson NJ;Down TA;Soranzo N
• 通讯作者: Soranzo N

The UK10K project identifies rare variants in health and disease.

• DOI: 10.1038/nature14962
• 发表时间: 2015-10-01
• 期刊: Nature
• 影响因子: 64.8
• 作者: UK10K Consortium;Walter K;Min JL;Huang J;Crooks L;Memari Y;McCarthy S;Perry JR;Xu C;Futema M;Lawson D;Iotchkova V;Schiffels S;Hendricks AE;Danecek P;Li R;Floyd J;Wain LV;Barroso I;Humphries SE;Hurles ME;Zeggini E;Barrett JC;Plagnol V;Richards JB;Greenwood CM;Timpson NJ;Durbin R;Soranzo N
• 通讯作者: Soranzo N