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下一代基因组数据生成、分发和可视化工具。

Next generation tools for genomic data generation, distribution, and visualization.

机构信息

Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, USA.

出版信息

BMC Bioinformatics. 2010 Sep 9;11:455. doi: 10.1186/1471-2105-11-455.

DOI:10.1186/1471-2105-11-455
PMID:20828407
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2944281/
Abstract

BACKGROUND

With the rapidly falling cost and availability of high throughput sequencing and microarray technologies, the bottleneck for effectively using genomic analysis in the laboratory and clinic is shifting to one of effectively managing, analyzing, and sharing genomic data.

RESULTS

Here we present three open-source, platform independent, software tools for generating, analyzing, distributing, and visualizing genomic data. These include a next generation sequencing/microarray LIMS and analysis project center (GNomEx); an application for annotating and programmatically distributing genomic data using the community vetted DAS/2 data exchange protocol (GenoPub); and a standalone Java Swing application (GWrap) that makes cutting edge command line analysis tools available to those who prefer graphical user interfaces. Both GNomEx and GenoPub use the rich client Flex/Flash web browser interface to interact with Java classes and a relational database on a remote server. Both employ a public-private user-group security model enabling controlled distribution of patient and unpublished data alongside public resources. As such, they function as genomic data repositories that can be accessed manually or programmatically through DAS/2-enabled client applications such as the Integrated Genome Browser.

CONCLUSIONS

These tools have gained wide use in our core facilities, research laboratories and clinics and are freely available for non-profit use. See http://sourceforge.net/projects/gnomex/, http://sourceforge.net/projects/genoviz/, and http://sourceforge.net/projects/useq.

摘要

背景

随着高通量测序和微阵列技术成本的迅速降低和可用性的提高，在实验室和临床中有效利用基因组分析的瓶颈正逐渐转移到有效管理、分析和共享基因组数据上。

结果

我们在此介绍了三个开源的、与平台无关的软件工具，用于生成、分析、分发和可视化基因组数据。这些工具包括下一代测序/微阵列实验室信息管理系统和分析项目中心（GNomEx）；一个使用社区认可的 DAS/2 数据交换协议（GenoPub）注释和编程分发基因组数据的应用程序；以及一个独立的 Java Swing 应用程序（GWrap），它为那些喜欢图形用户界面的人提供了尖端的命令行分析工具。GNomEx 和 GenoPub 都使用富客户端 Flex/Flash 网页浏览器界面与远程服务器上的 Java 类和关系数据库进行交互。它们都采用了公共-私人用户组安全模型，能够在控制患者和未发表数据的同时与公共资源一起分发。因此，它们可以作为基因组数据存储库，通过启用 DAS/2 的客户端应用程序（如 Integrated Genome Browser）手动或编程访问。

结论

这些工具在我们的核心设施、研究实验室和临床中得到了广泛的应用，并可免费用于非营利性用途。请访问 http://sourceforge.net/projects/gnomex/、http://sourceforge.net/projects/genoviz/ 和 http://sourceforge.net/projects/useq。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a033/2944281/d7da0e4309cc/1471-2105-11-455-11.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a033/2944281/f0a13d62db4e/1471-2105-11-455-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a033/2944281/7880549853e1/1471-2105-11-455-3.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a033/2944281/90ab7684f369/1471-2105-11-455-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a033/2944281/ca26af4378de/1471-2105-11-455-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a033/2944281/7f5a2880a0ef/1471-2105-11-455-7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a033/2944281/f4c97ae1f689/1471-2105-11-455-8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a033/2944281/2f29e54658c6/1471-2105-11-455-9.jpg
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