INBRE BIOINFORMATICS CORE

本子项目是利用由NIH/NCRR资助的中心赠款提供的资源的众多研究子项目之一。子项目和研究者（PI）可能已经从另一个NIH来源获得了主要资金，因此可以在其他CRISP条目中表示。列出的机构是中心的，不一定是研究者的机构。特拉华州布林公司2006年年度进展报告（APR）批准号5P20RR016472-2006生物信息学核心特拉华州布林公司生物信息学核心正在继续扩展和升级布林公司/布林公司项目下的硬件、软件和人员基础设施。在INBRE二年级期间，随着BRIN/INBRE的重点从基础设施实施转移到研究能力发展，所有合作机构都专注于教育活动和应用程序改进。此外，随着研究人员将生物信息学作为一种强大的研究工具加以改进，基础设施投资开始产生重大的科学进展。此外，在今年，生物信息学核心重点是加强INBRE合作机构在全州范围内对互联网2的访问；改善获取生物信息学软件和专业知识的途径，并开展协调一致的教育活动，如提高生物信息学素养的讲习班。仅在过去的一年里，来自INBRE网络的大约20名教职员工及其研究小组直接受益于DBI的生物信息学中心。大量的生物信息学和计算生物学资源现已到位，以支持特拉华州INBRE网络中所有合作机构的研究和教学。生物信息学核心在第二年的成就包括：生物信息学基础设施和管理升级：1)DBI正在进行一个项目，该项目旨在标准化中心内数据库的管理方式。完成后，查看和/或操作存储数据的接口可以在更短的时间内实现，从而缩短数据生成和使用之间的窗口。2)生物信息学中心正在最后安装一个软件门户，以便INBRE网络的所有成员方便地访问大量的计算资源。该门户将允许用户向计算服务器队列提交新的计算作业，并改善对广泛的生命科学和生物医学软件程序的访问。3)根据与特拉华大学的协议，将特拉华州立大学作为赞助参与者纳入第二代互联网联盟。这次扩建将为DSU的整个校园提供更多的访问机会，并将为DSU的教职员工和研究人员提供更好的研究机会。4)特拉华州科学与应用计算中心（DeSAC）在DSU由INBRE资助发起，支持更广泛的大学社区，并与外部研究机构合作，支持与生物医学研究相关的计算项目。DESAC中心工作人员还支持特拉华州立大学生物信息学课程和生物技术研究人员的信息技术需求。5)由INBRE和COBRE资助购买的DBI生物信息学中心的128节点双处理器Sun Biowolf计算集群获得升级，增加了96GB内存。这将提高集群的性能，具有更大的基因组搜索吞吐量。6)将CAVE系统从5年前的SGI Onyx系统升级到高性能的SGI Prism服务器。这次升级的资金是由能源部拨款提供的。研究成果和正在进行的项目：特拉华大学植物分子生物学研究人员Pam Green和Blake Meyers应用了一种新的测序方法，该方法涉及使用生物信息学中心的128节点双处理器Biowolf计算服务器进行数据分析。迈耶斯和格林正在研究拟南芥中的小rna，通过他们的方法，他们能够识别出77000个rna。在他们合作之前，由于之前的过程缓慢且费力，只鉴定了6000个小rna。生物信息学基础设施工具有助于加速小RNA鉴定过程，这是确定其功能的第一步。在这项工作的基础上，进一步的工作也开始在哺乳动物细胞中研究小rna。生物信息学中心的数据库管理员Leo Genyuk一直与杜克大学的几位研究人员密切合作，包括Blake Meyers博士在一个名为“大规模平行特征测序”（MPSS）的项目上，以及海洋研究学院的Eric Wommack博士在一个名为“浮游生物生态学微生物观测站”（MOVE）的项目上。这两个项目都从Genyuk先生在Oracle数据库方面的详细专业知识中受益匪浅。这种专门知识将继续扩展到与INBRE生物医学研究议程有关的其他项目。生物医学可视化研究在DBI和Christiana Care的研究人员之间进一步发展，重点是虚拟手术和医学图像可视化，以及复杂数据库分析的多变体可视化，如Christiana Care的早期肺癌行动计划（ELCAP），以及多种生物体之间的基因组信息可视化。来自Christiana Care的Michael Teixido医生与DBI的Karl Steiner医生密切合作，对内耳进行了非常详细的可视化。这种可视化将用于耳鼻喉科医生的解剖教育，并将导致内耳相关疾病的治疗选择，如良性阵发性位置性眩晕（BPPV），胆脂瘤的手术治疗和人工耳蜗植入手术方面的评估。此外，Steiner博士还担任Christiana Care的Tomas Bauer博士的导师，并担任博士生Raymond Chen和三名inbre支持的本科生实习生的顾问，以扩展应用程序，包括虚拟手术模拟中触觉设备的集成以及CT和MRI扫描的持续可视化。教育和研讨会：1)2005年5月，DBI主办了由OpenHelix提供的三种主要基因组浏览器的介绍。为期一天的研讨会提供了概述和实践环节，重点介绍了Ensembl基因组浏览器、UCSC基因组浏览器和NCBI地图查看器。2)2005年6月，DBI生物信息学经理Doug O¿Neal与Sun Microsystems合作，在底特律ISMB会议上介绍了计算机网格技术的使用。3)生物信息学中心参加了2005年11月11日在DBI举行的核心中心开放日。开放日活动包括所有核心中心主任的演讲，随后是参观和实验室演示。来自整个网络的30多名与会者参加了此次活动。根据积极的反馈，这个活动现在将每年举行一次。

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. Delaware BRIN Annual Progress Report (APR) 2006 Grant No. 5P20RR016472-2006 Bioinformatics Core The Delaware INBRE Bioinformatics Core is continuing to expand and upgrade the hardware, software and personnel infrastructure put in place under the BRIN/INBRE programs. During INBRE Year 2, all partner institutions have focused on education activities and application improvement as the BRIN/INBRE focus shifts from infrastructure implementation to research competency development. Furthermore, the infrastructure investment is beginning to produce significant scientific progress as investigators refine their use of bioinformatics as a powerful research tool. Also during this year the Bioinformatics Core has focused on enhanced statewide access to Internet 2 for INBRE partner institutions; improved access to bioinformatics software and expertise, and on coordinated educational events such as workshops to improve bioinformatics literacy. Over the past year alone, some 20 faculty members and their research groups from across the INBRE Network directly benefited from the Bioinformatics Center at DBI. Substantial bioinformatics and computational biology resources are now in place to support research and teaching at all partner institutions in the Delaware INBRE network. Accomplishments of the Bioinformatics Core in Year 2 include: Bioinformatics Infrastructure and Management Upgrades: 1) DBI is midway through a project to standardize the way databases are managed within the Center. Upon completion, interfaces to view and/or manipulate stored data can be implemented in a much shorter time frame, allowing for a shorter window between when data is generated and when it can be used. 2) The Bioinformatics Center is finalizing installation of a software portal to ease access to the considerable computing resources for all members of the INBRE Network. This portal will allow users to submit new computing jobs into the computing server queue and also to improve access a broad set of life sciences and biomedical software programs available. 3) Integration of Delaware State University in the Internet2 consortium as a sponsored participant under an agreement with the University of Delaware. This expansion will provide expanded access to the entire campus at DSU and will facilitate better research access for the faculty and researchers at DSU. 4) The Delaware Center for Scientific and Applied Computation (DeSAC) initiated at DSU with INBRE funding supported the broader University community and collaborated with external research agencies in support of computation projects related to biomedical research. The DESAC Center staff also supported the information technology needs of the Delaware State University Bioinformatics courses and the biotechnology researchers. 5) The Sun Biowolf Compute Cluster, a 128-node dual processor in the DBI Bioinformatics Center purchased with INBRE and COBRE funding, received an upgrade with the addition of 96GB of memory. This will increase the performance of the cluster, with a much greater throughput of genomic searches. 6) Upgrade of the CAVE system from a five-year old SGI Onyx system to a high-performance SGI Prism server. Funding for this upgrade was provided by a grant from the Department of Energy. Research Accomplishments and Ongoing Projects: University of Delaware plant molecular biology researchers Pam Green and Blake Meyers have applied a novel sequencing approach that involves data analysis using the 128-node dual processor Biowolf Compute Server in the Bioinformatics Center. Meyers and Green are investigating small RNAs in the plant Arabidopsis, and through their approach were able to identify 77,000 RNAs. Before their work together, only 6,000 small RNAs had been identified, since the previous process was slow and labor-intensive. Bioinformatics infrastructure tools have helped accelerate the small RNA identification process, which is the first step to determining their function. Based on this work, additional work has been started to pursue small RNAs in mammalian cells as well. Database Administrator Leo Genyuk in the Bioinformatics Center has been collaborating closely with several UD researchers including Dr. Blake Meyers on a project entitled Massively Parallel Signature Sequencing (MPSS) ¿ as described above- and Dr. Eric Wommack from the College of Marine Studies on a project entitled Microbial Observatory for Virioplankton Ecology (MOVE). Both of these projects benefited highly from Mr. Genyuk¿s detailed expertise in Oracle databases. This expertise will continue to expand for additional projects related to the biomedical research agenda of the INBRE. Biomedical visualization research grew further between researchers at DBI and at Christiana Care with an emphasis on virtual surgery and medical image visualization and on multi-variant visualization of complex database analysis such as Christiana Care's Early Lung Cancer Action Program (ELCAP) and for genomic information visualization between multiple organisms. Dr. Michael Teixido from Christiana Care worked closely with Dr. Karl Steiner at DBI on a highly detailed visualization of the inner ear. This visualization will be used for the anatomical education of otolaryngologists and will lead to treatment options for inner ear related medical conditions such as Benign Paroxysmal Positional Vertigo (BPPV), to surgical treatment of Cholesteatoma and the evaluation of surgical aspect of cochlear implantation. In addition, Dr. Steiner served as mentor to Dr. Tomas Bauer of Christiana Care, and as advisor to Ph.D. student Raymond Chen and three INBRE-supported undergraduate student interns to expand applications including the integration of haptic devices in virtual surgery simulation and continued visualization of CT and MRI scans. Education and Seminars: 1) In May 2005, DBI hosted an Introduction to Three Major Genome Browsers presented by OpenHelix. The daylong workshop offered both an overview and hands-on session featuring the Ensembl Genome Browser, the UCSC Genome Browser, and the NCBI Map Viewer. 2) In June 2005, DBI Bioinformatics Manager Doug O¿Neal collaborated with Sun Microsystems to present a tutorial at the ISMB conference in Detroit on the use of computer grid technology. 3) The Bioinformatics Center participated in the Core Center Open House held at DBI on November 11, 2005. The Open House event included presentations by all Core Center directors and was followed by tours and demonstrations in the labs. Over 30 attendees from across the Network attended the event. Based on the positive feedback, this event will now be held on an annual basis.