INBRE BIOINFORMATICS CORE

INBRE 生物信息学核心

• 批准号: 7381586
• 负责人: KARL V. STEINER
• 金额: $ 92.53万
• 依托单位: UNIVERSITY OF DELAWARE
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-05-01 至 2007-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7381586
• 关键词: INBRE; BIOINFORMATICS; CORE

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.