WHOLE GENOME ASSEMBLY FROM NEXTGEN SEQUENCING SHORT READ DATA

来自下一代测序短读数据的全基因组组装

• 批准号: 8364347
• 负责人: CECILIA W. LO
• 金额: $ 0.11万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-15 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8364347
• 关键词: Address; Algorithms; Benchmarking; Biomedical Research; CLC Gene; Client; Computer software; Data; Development; Funding; Genome; Genomics; Grant; High Performance Computing; Licensing; Modeling; National Center for Research Resources; Occupations; Principal Investigator; Production; Reading; Research; Research Infrastructure; Research Proposals; Research Support; Resources; Running; Solutions; Source; Supercomputing; Testing; Time; United States National Institutes of Health; Work; abstracting; analytical tool; cell assembly; cost; next generation; parallel processing; software systems; tool; user-friendly

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Request: 30,000 SUs and 12 months Advanced User Support Abstract: This startup project will explore how best to leverage Blacklight at the Pittsburgh Supercomputing Center for next-generation sequencing data and genome analysis applications. The following software systems will be installed, and appropriate components selected, tested and benchmarked to enable the development of a TeraGrid research proposal: (1) Applied Biosystems Bioscope package. (2) CLC Bio software. Both ABI and CLC will support this project with trial licenses and developer expertise. Below we provide additional background on these two packages. AB Bioscope - This package was installed and run successfully during the friendly user period on Blacklight. There were some efficiency issues, which will be addressed when Blacklight enters production in early January. CLC Bio Genomics Workbench / server -The CLC software is split into a server and clients. Both have essentially identical analytical tools from the user perspective, but the server allows clients to initiate multiple jobs at once (whereas the clients are limited to single jobs at a time, typically). The server is what we run in our lab. The CLC Genomics server can queue multiple jobs at once, and with multiple nodes attached, can parallel process jobs. The "client" Workbenches are graphical, wizard driven tools that are relatively simple for biologists to run. This can run in X-windows. The clients function as very capable desktop solutions, but can also be the "client" when you have access to the CLC Bio server solution. CLC Bio Assembly Cell - This is the CLC Bio command line product, where CLC Bio first implements new development in these algorithms after which they get migrated to both the CLC Genomics Workbench, and the Genomics Server products. We plan to focus on this first, and see how it could support research that could only be done on Blacklight. Then we will investigate how Blacklight can fit into the Client-Server model. We have obtained a trial license for this product, for our tests on Blacklight. Advanced User Support During the friendly user period we have worked with Drs. Jana and Sanielevici at PSC. Their continued support of our work will be very important during this startup project.

这个子项目是利用资源的许多研究子项目之一。 由NIH/NCRR资助的中心拨款提供。对子项目的主要支持 子项目的首席调查员可能是由其他来源提供的， 包括美国国立卫生研究院的其他来源。为子项目列出的总成本可能 表示该子项目使用的中心基础设施的估计数量， 不是由NCRR赠款提供给次级项目或次级项目工作人员的直接资金。 申请：30,000个SU和12个月的高级用户支持摘要：这个初创项目将探索如何最好地利用匹兹堡超级计算中心的Blacklight进行下一代测序数据和基因组分析应用。将安装下列软件系统，并选择、测试和确定适当的组件，以支持TeraGrid研究提案的开发：(1)应用生物系统生物观察包。(2)CLC Bio软件。ABI和CLC都将以试验许可证和开发人员的专业知识支持该项目。下面我们将提供有关这两个包的其他背景。AB Bicope-在Blacklight的友好用户期间成功安装并运行了此程序包。有一些效率问题，当Blacklight在1月初投产时，这个问题将得到解决。CLC生物基因组学工作台/服务器-CLC软件分为服务器和客户端。从用户角度来看，两者具有基本相同的分析工具，但服务器允许客户端一次启动多个作业(而客户端通常一次只能启动一个作业)。服务器就是我们在实验室中运行的服务器。CLC基因组学服务器可以一次对多个作业进行排队，并且连接了多个节点，可以并行处理作业。“客户”工作台是图形化的、由向导驱动的工具，对于生物学家来说运行起来相对简单。它可以在X-Window中运行。客户端功能非常强大的桌面解决方案，但也可以是“客户端”，当您有权访问CLC生物服务器解决方案。CLC Bio Assembly Cell-这是CLC Bio命令行产品，CLC Bio首先在这些算法中实施新的开发，之后它们被移植到CLC基因组学工作台和基因组学服务器产品。我们计划首先关注这一点，看看它如何支持只能在Blacklight上完成的研究。然后，我们将研究Blacklight如何适应客户端-服务器模型。我们已经获得了该产品的试用许可证，用于我们在Blacklight上的测试。高级用户支持在友好的用户期间，我们与PSC的Jana和Sanilevici博士一起工作。在这个初创项目中，他们对我们工作的持续支持将是非常重要的。