INBRE BIOINFORMATICS CORE

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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 INBRE Annual Progress Report (APR) 2007 Grant No. 5P20RR016472-2007 Bioinformatics Core The Delaware INBRE Bioinformatics Core is consolidating the hardware, software and personnel infrastructure put in place under the BRIN/INBRE programs. During INBRE Year 3, 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. Over the past year alone, about 15 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 in place to support research and teaching at all partner institutions in the Delaware INBRE network. Accomplishments of the Bioinformatics Core in Year 3 include: Bioinformatics Infrastructure and Management Upgrades: 1) DBI is working to standardize the way databases are managed within the Center. The Center is emphasizing the advantages of centralizing the storage and management of laboratory data within the controlled environment of the DBI database systems. 2) The Bioinformatics Center's software portal is in place to researchers who are unfamiliar with the details of the interfaces into the computing servers. The portal allows web-based access to the life sciences and biomedical software programs available on the DBI servers. 3) The Bioinformatics Center is in the process of upgrading the Sun database server from a single multi-processor system to a dedicated cluster of servers. Performance of the databases will be enhanced by this upgrade, along with increases in overall data availability and ease of future upgrades. 4) The backup server for the Bioinformatics Center is being changed from a tape-based system to a paired set of servers, one on-site and one off-site, capable of on-line backups. With 24TB of disk storage each, the Center's servers will have data backed up to fast storage, reducing the backup window and greatly decreasing the time to restore lost data. 5) The Bioinformatics Center has been heavily involved in the development of an on-line evaluation interface to provide a more reliable and easier-to-use evaluation process for the INBRE program. Faculty and students are asked to use this interface to help in the evaluation of events, to collect data on publication and presentation and to provide feedback on such issues as core centers or mentoring. 6) The Bioinformatics Center participated in the Core Center Open House that was held at DBI on September 29, 2006. The Open House event included presentations by all Core Center directors and was followed by tours and demonstrations in the labs. Attendance doubled from the previous year to 62 attendees representing all institutions across the Network. The Open House presentations were video-streamed live across the recently installed INBRE-supported videoconference system. An archived copy of the Open House and of other research presentations is available on the DBI web under www.dbi.udel.edu/events/luncheons.html. 7) Dr. Mihailo Kaplarevic has been hired as a Database Programmer in the Bioinformatics Center. With experience in parallel computing, data mining and informational systems design and development, his collaboration with resident researchers will tailor the Center's resources to ongoing projects. Specific collaborations will be with Dr. Blake Meyers on a project entitled Massively Parallel Signature Sequencing (MPSS), Dr. Eric Wommack from the College of Marine Studies on a project entitled Microbial Observatory for Virioplankton Ecology (MOVE), and Dr. Guang Gao from the Department of Electrical and Computer Engineering. 8) Internet2 went live at Delaware State University (DSU) in April 2006. The campus is fully and transparently connected to Internet2. DSU selected Verizon to provide dedicated connectivity to the University of Delaware. The University of Delaware purchased additional bandwidth to MAGPI (Mid-Atlantic Gigapop in Philadelphia for Internet2) that is now being channeled to at a fraction of the cost of a direct connection to MAGPI. The University of Delaware is sponsoring DSUs participation in the Internet2 consortium. This level of membership offers the same level of service as any other membership level, but no eligibility to vote in Internet2 consortium matters. DSU is connected to Internet2 though a 45Mbps connection with a provision to purchase (temporary or permanent) additional bandwidth at anytime. The monthly cost of connection has already been transferred to DSUs operating budget. 9) The laboratory of the Delaware Scientific and Advanced Computing Center (DeSAC) at DSU consists of SUN workstations and a fileserver that provides access to the Accelrys GCG software. This software package includes a number of sequence matching algorithms that operate on associated gene sequence databases. A bioinformatics course for undergraduate students is being taught Spring 2007, using DeSAC software and workstations. DSU is starting to tackle the challenge of getting more biomedical research faculty and graduate students to integrate both DeSAC capabilities and experimentation in their research programs. Research Accomplishments and Ongoing Projects: Biomedical visualization research grew further between researchers at DBI and at Christiana Care with an emphasis on virtual surgery and medical image visualization. The visualization effort builds on the capabilities of the Visualization Studio at DBIs Bioinformatics Center. Currently, four faculty members are involved in this effort: Dr. Karl Steiner, Associate Director of DBI and Professor of Electrical and Computer Engineering at UD, Dr. Ken Barner, Professor of Electrical and Computer Engineering at UD, Dr. Chandra Kambhamettu, Associate Professor of Computer and Information Sciences at UD, and Dr. Fengshan Liu, Professor of Computer Sciences at DSU. Drs. Kambhamettu and Liu are conducting two of the INBRE-supported research projects, in the area of ground glass opacity lung tumor detection and simulations of breast surface deformations during mammography, respectively. Dr. Barner, Dr. Kambhamettu and Dr. Steiner are working closely with Dr. Tom Bauer at Christiana Care on a project to create accurate and real-time haptic and visual feedback from biomedical simulations. The long-term goal is to create a virtual surgery simulator and current work is focused on the extraction and segmentation of organs from CT or MRI-based scans and on the collision detection and tactile haptic feedback from interactions with these biomedical models. Dr. Michael Teixido from Christiana Care worked closely with Dr. Steiner 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. BPPV is a common cause of dizziness caused by debris, consists of small crystals of calcium carbonate, which has collected within a part of the inner ear. BPPV is responsible for 20% of all dizziness and 50% of dizziness in the elderly and a leading cause of falls and fractures in older patients. Once the physician has successfully diagnosed the location of abnormally positioned otoliths through careful observation of the eye movements of the patient as they perform specific head motions, this virtual-reality simulator will allow them to demonstrate and practice the appropriate combination of head movements required to treat the affected canal(s). The BPPV viewer is available on the web under www.dbi.udel.edu/People/teixido.html. The 3-D model of the human labyrinths provides an effective teaching tool for students and clinicians treating patients with balance disorders. The Center's expertise in providing computing resources was recognized by John Wiley & Sons to invite DBI Bioinformatics Manager Dr. Douglas O'Neal to contribute an article to their Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics on Grid Technologies. This article was published October 15, 2006.