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.

该子项目是利用资源的众多研究子项目之一 由 NIH/NCRR 资助的中心拨款提供。子项目的主要支持 并且子项目的主要研究者可能是由其他来源提供的， 包括其他 NIH 来源。 子项目可能列出的总成本 代表子项目使用的中心基础设施的估计数量， NCRR 赠款不直接向子项目或子项目工作人员提供资金。 请求：30,000 个 SU 和 12 个月的高级用户支持 摘要：该启动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。将安装以下软件系统，并选择、测试和基准测试适当的组件，以实现 TeraGrid 研究计划的开发： (1) Applied Biosystems Biscope 软件包。 (2)CLC Bio软件。 ABI 和 CLC 都将通过试用许可证和开发人员专业知识来支持该项目。下面我们提供了这两个包的更多背景信息。 AB Biscope - 该软件包已在 Blacklight 的友好用户期间成功安装并运行。存在一些效率问题，这些问题将在 Blacklight 一月初投入生产时得到解决。 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。从用户的角度来看，两者具有本质上相同的分析工具，但服务器允许客户端一次启动多个作业（而客户端通常一次仅限于单个作业）。服务器是我们在实验室中运行的。 CLC Genomics 服务器可以同时对多个作业进行排队，并且连接多个节点后，可以并行处理作业。 “客户端”工作台是图形化、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-windows 中运行。客户端可作为非常强大的桌面解决方案，但当您可以访问 CLC Bio 服务器解决方案时，也可以作为“客户端”。 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开发，然后将它们迁移到 CLC Genomics Workbench 和 Genomics Server 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。我们已获得该产品的试用许可证，用于 Blacklight 测试。高级用户支持 在友好用户期间，我们与 Drs 一起工作。 PSC 的 Jana 和 Sanielevici。在这个启动项目期间，他们对我们工作的持续支持将非常重要。