CORE D: BIOINFORMATICS CORE

核心 D：生物信息学核心

• 批准号: 7336118
• 负责人: JAMES M BOWER
• 金额: $ 32.8万
• 依托单位: UNIVERSITY OF TEXAS SAN ANTONIO
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-08-01 至 2007-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7336118
• 关键词: CORE; BIOINFORMATICS

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The overall objective of the proposed Core in Computational Biology and Bioinformatics is to provide a world-class facility supporting the research of current as well as future biologists at UTSA as well as the training of our students. The two specific aims identified in the original proposal were to 1) Establish a Bioinformatics core facility and 2) Support Computational Biology. While the software, hardware and personnel involved in supporting each activity are somewhat different ? the essential infrastructure requirements for each are shared, and are therefore described together in the following sections:Considerable progress has been made on the establishment of this core facility. First, we have established an organizational structure, which includes both internal and external advisory committees. Second, we have designed a University-wide questionaire to determine current support needs for faculty and student research. That survey will be administered through the facilities new web-site. www.sa-comp-bio.org. Third, the University has allocated approximately 3,500 square feet dedicated solely to this facility on the first floor of the new BioSciences and Engineering Building slated for completion in the fall of 2005. We have worked with the university to establish a design for this facility which includes specially equiped space for the Beowolf computing cluster, general users space for workstations, conference space for training, data review and collaboration, as well as office space for facility staff, including the director.With respect to personnel, UTSA is now engaged in a nationwide search for a director for the facility. The job description was been posted through the UTSA HR system, and the facility P.I.s have posted the position through many email groups. Applications have begun to be recieved. We anticipate having the director on board in mid-summer.While we are searching for the best possible director, the P.I.s have already begun installing hardware and software to support our basic mission. Specifically, we have purchased two workstations (one supporting Windows, and one supporting the Macintosh opperating system), and have hired personnel to begin installing a wide range of computational software. We have been accumulating and installing relevant computational free-ware on these machines. In addition, software licenses have been securred for the full Matlab service, Genespring service, and Mathematica service. Particular attention has been paid to coordinating our facility to support the data processing needs of the other RCMI core facilities (Imaging, Genomics, Proteonmics) and a committee has been established with representation from these other core facilities to assure smooth coordination. We have recently obtained the Bit Plane software package, which will be important for analysis of data obtained by the imaging core, and we have obtained a service license for the Genespring software package, which we discovered in the process had been purchased seperately by three different UTSA laboratories. Adding this software to the facility saved each of these labs considerable expense and has resulted in better coordination of the use of the software. We have also provided support for the Affymetrix service contract in support of the genomics core facility. Although money is not allocated for purchase of the computing cluster until the second year, we have begun the process of specifying our advanced computing needs, and working with vendors to obtain the best possible computational cluster for the facility. We have engaged the services of Mr. Greg Hood at the Pittsbourgh Super Computing Center, a specialist in parallel computing applications in biology. We have meet with several vendors (Dell Computer, Sun Microsystems) and are working with these vendors for competitive bids. Finally, from April 30 ? May 1st, we organized the first International Biologically Accurate Modeling Meeting in San Antonio, attended by 125 computational biologists from around the world (the US, England, India, Germany, Sweeden, Armenia, Brazil, Mexico). UTSA faculty and student attended and made presentations at this meeting, which will now be held annually in the spring in San Antonio. This meeting will considerably raise the visibility of the RCMI computational Core.

该子项目是利用NIH/NCRR资助的中心赠款提供的资源的许多研究子项目之一。子弹和调查员（PI）可能已经从其他NIH来源获得了主要资金，因此可以在其他清晰的条目中代表。列出的机构适用于该中心，这不一定是调查员的机构。拟议的核心在计算生物学和生物信息学方面的总体目标是提供世界一流的设施，以支持UTSA当前以及未来生物学家的研究以及对学生的培训。原始建议中确定的两个具体目的是1）建立生物信息学核心设施和2）支持计算生物学。而涉及支持每项活动的软件，硬件和人员却有所不同？每个人共享的基本基础架构要求，因此在以下各节中一起描述：在建立此核心设施方面取得了很大进展。首先，我们建立了一个组织结构，其中包括内部和外部咨询委员会。其次，我们设计了一个范围内的问题，以确定当前的教师和学生研究的支持需求。该调查将通过设施进行新的网站进行管理。 www.sa-comp-bio.org。第三，该大学已分配了大约3500平方英尺，仅专门用于新的生物科学和工程大楼的一楼，该设施计划于2005年秋天完成。我们与该设施合作，为该设施建立了设计，该设施为Beowolf Computs，用于培训，培训，数据，培训的空间以及培训，以及培训的空间，包括培训，数据，包括培训，以及培训，以及培训，数据，数据，以及数据，培训，以及培训，数据，以及数据在人员方面，UTSA现在正在全国范围内寻找该设施的董事。职位描述是通过UTSA HR系统发布的，该设施P.I.S已通过许多电子邮件组发布了职位。申请已开始收到。我们预计将在仲夏登机。当时我们正在寻找最佳的董事，但P.I.S已经开始安装硬件和软件来支持我们的基本任务。具体来说，我们购买了两个工作站（一个支持窗口，另一个支持Macintosh操作系统），并雇用了人员开始安装广泛的计算软件。我们一直在这些计算机上积累和安装相关的计算免费软件。此外，软件许可已被证券用于完整的MATLAB服务，Genespring Service和Mathematica服务。特别注意协调我们的设施，以支持其他RCMI核心设施（成像，基因组学，蛋白质学）的数据处理需求，并建立了一个委员会，并从这些其他核心设施的代表人数中确保了平稳的协调。我们最近获得了BIT平面软件包，这对于分析由成像核心获得的数据很重要，并且我们获得了Genespring软件包的服务许可，我们在此过程中发现的是由三个不同的UTSA实验室单独购买的。将此软件添加到该设施中，节省了这些实验室的大量费用，并可以更好地协调软件的使用。我们还为支持基因组核心设施的Affymetrix服务合同提供了支持。尽管直到第二年才分配资金用于购买计算集群，但我们已经开始指定我们的先进计算需求，并与供应商合作，以获取该设施的最佳计算集群。我们已经在Pittsbourgh超级计算中心（Pittsbourgh Super Computing Center）聘用了Greg Hood先生的服务，这是生物学中并行计算应用专家的服务。我们与几家供应商（Dell Computer，Sun Microsystems）会面，并正在与这些供应商合作以获得竞争性投标。终于，从4月30日起？ 5月1日，我们在圣安东尼奥组织了第一次国际生物学上的建模会议，由来自世界各地的125名计算生物学家（美国，英格兰，印度，德国，德国，斯威登，亚美尼亚，亚美尼亚，巴西，墨西哥）参加。 UTSA教师和学生在这次会议上参加并进行了演讲，该会议现在将在春季在圣安东尼奥举行。这次会议将大大提高RCMI计算核心的可见性。