This subproject is one of many research subprojects utilizing theresources provided by a Center grant funded by NIH/NCRR. The subproject andinvestigator (PI) may have received primary funding from another NIH source,and thus could be represented in other CRISP entries. The institution listed isfor the Center, which is not necessarily the institution for the investigator.Delaware INBRE Annual Progress Report (APR) 2008Grant No. 5P20RR016472-07Bioinformatics Core The goal of the Delaware INBRE Bioinformatics Core is to position Delaware to provide resources and expertise in the areas of bioinformatics, computational and systems biology to enable Delaware's faculty to become nationally competitive in biomedical research. To meet that goal bioinformatics labs have been implemented at all of the academic partner institutions, i.e. the Delaware Biotechnology Institute at the University of Delaware (DBI), Delaware State University (DSU), Wesley College and Delaware Technical & Community College (DTCC). In addition, a unique network of biomedical visualization centers has been installed at Christiana Care, DBI, DSU and DTCC.The Bioinformatics (BioIT) Center at DBI serves as the hub for many of the activities in the bioinformatics core. It is managed by Dr. Douglas O'Neal and provides professionally expertise in high-performance computation, database analysis and image visualization.The BioIT Center has integrated significant hardware and software resources into a reliable and unified system. Within this system, compute, database and visualization servers are transparently working with each other to provide secure access to researchers across the INBRE Network. The BioIT Center continues to provide resources for computing and database needs of INBRE researchers, with about ten research groups running code on the compute cluster, four groups using the database cluster, four groups hosting their servers in the Core's computer room, three groups utilizing the Visualization studio and the Core's email and web servers servicing a broad range of users.Accomplishments of the Bioinformatics Core in Year 7 include:Development of a Statewide Cyberinfrastructure Plan+ Delaware research institutions have developed a plan to improve the State's cyber-infrastructure to better meet the needs of the INBRE community. This plan is focused on five main objectives: (1) Strengthen capacity and capability of cyber-knowledgeable faculty and staff; (2) Provide a strong computational capability that is easily accessible to all members in the Network; (3) Develop regional collaborations to take advantage of expertise and capabilities in partner states; (4) Develop a high-throughput genomics research capability; and (5) Provide collaborative research capabilities at the desktop level.+ Due to its central location on the Mid-Atlantic Coast and close proximity to major population centers such as Philadelphia, PA and Baltimore, MD, Delaware's cyberinfrastructure is well positioned. The graph provided above shows an overview of the status of Delaware's network connectivity. With support by the NIHINBRE and the NSFEPSCoR RII program, all of the partner institutions have put in place dedicated centers or classrooms to support bioinformatics research and learning activities. In comparison to many other IDeA states, Delaware's connectivity to the Nation's broadband networks (Abilene and National LambdaRail) is in good condition. There is, however, a continuing need to further improve desktop access for researchers at many of Delaware's INBRE partner institutions. The most pressing need is for more cyberinfrastructure personnel that can provide faculty and students with the necessary expertise to utilize many of the tools already available to Delaware researchers, including complex data visualization and access to parallel computing and database resources both in-state and through the grid. Listed below are updates to each of the strategic objectives outlined above: (1) Strengthening Bioinformatics Faculty at Delaware Institutions+ The University of Delaware is currently searching for the Edward G. Jefferson Endowed Chair in Bioinformatics and Computational Biology, who will have the responsibility to build a coherent bioinformatics network across UD and across the State and lead the search for three additional junior faculty members. This initiative will provide much needed expertise for the growing INBRE Network. These new faculty members will be augmented by an experienced group of staff scientists and engineers at the DBI Bioinformatics (BioIT) Center.+ Delaware State University is finalizing plans to hire two new faculty members with expertise in bioinformatics and biostatistics. These two faculty members will collaborate with each other and with research teams across institutions. The biostatistics faculty fills a much-needed gap in faculty expertise at DSU. The bioinformaticist will facilitate DSU goals by implementing technologies, integrating into existing networks, and collaborating with DSU experimentalists to incorporate bioinformatics techniques and resources into their research. These searches will be launched within the next two years. (2) Bioinformatics Infrastructure and Management Upgrade+ Database services have been migrated to a cluster of six servers allowing for higher performance and reliability. Performance gains on single-server applications have been seen but major speedups are possible with the parallelization of database queries across multiple servers. In one production application, query times have been reduced by two orders of magnitude by re-writing the application to use multiple servers in parallel.+ A database system has been installed for use by the Bioimaging Core, where data from various microscopes can be uploaded, annotated, and shared though a web interface. Approximately .5 TB of image data is currently being shared though this system.+ As described above, the Linux compute cluster has seen incremental upgrades. Seven of the original dual-core/2GB ram 32-bit servers have been replaced with quad-core/8GB ram 64-bit systems. Four more of the original servers were later replaced with one 16-core/64GB ram 64-bit server and one 16-core/128GB ram 64-bit server. The original file server for the cluster has been replaced with a newer server with higher hardware redundancy. Use of the 64-bit servers has allowed calculations on problems that were not possible with the architecture restrictions imposed by 32-bit hardware.+ Backup services to on-line storage have been extended to all data within the Core. An off-site copy of the backup data is created in real-time to allow for disaster recovery. + The Bioinformatics Core participated in the Core Center Open House that was held at DBI on October 5, 2007. The Open House even included presentations by all Core Center directors and was followed by tours and demonstrations in the centers. The Open House presentations were video-streamed live for viewing by interested researchers who were not able to attend.+ Core personnel implemented several programs to aid in evaluating grant metrics, creating tools to create, publish, and evaluate data from web-based surveys and on-line databases of information on persons associated with DBI grants.+ A web-based system for accepting student resumes and matching them to open research positions was brought online in the past year. Research Accomplishments and Ongoing Projects:+ The BioIT Center's Manager, Dr. Douglas O'Neal, was invited to participate on the Bioinformatics Panel at the Northeast Regional Life Sciences Core Directors Meeting held November 7-9, 2007 at Cornell University. This meeting brought together Core Directors from the Northeast Region as well as several other states and Canada.+ The BioIT Center's Database Programmer, Dr. Mihailo Kaplarevic, attended the Life Sciences Society Computational Systems Bioinformatics Conference held at San Diego August 13-17, 2007, presenting a poster titled 'Advanced Framework for Environmental Metagenome Analysis.' (3) NENI A Regional Cyberinfrastructure Collaboration among IDeA States+ The Delaware INBRE is leading a regional effort called Northeast Network Initiative (NENI) to systemically improve inter-institutional collaborations among academic and biomedical institutions in New Hampshire, Maine, Rhode Island, Vermont and Delaware. The NENI initiative will lead to the development of sustainable biomedical research capabilities by significantly enhancing connectivity for academic and medical institutions in the New England States and Delaware the members of the Northeastern IDeA Network. This fundamental infrastructure enhancement is required to provide a critical backbone for new collaborative research projects and provide remote access to core facilities in such areas as bioinformatics, bioimaging, sequencing or mass spectroscopy; facilitate remote videoconferencing and on-line streaming of workshops and seminars; and the development of joint research projects with faculty and students at institutions across the Northeastern States in the IDeA Network and across the nationwide IDeA community.+ The first regional NENI Workshop was held during the 2nd Northeast Regional IDeA meeting in Burlington, VT on August 17, 2007. During this meeting the members of the NENI Executive Council presented an overview of the Initiative and then individual updates on the needs, status and activities within each NENI state. + As a direct outcome of the workshop and the NENI initiative, the NENI states competed for an INBRE Administrative Supplement in fall 2007 and secured about $550k from NIH-NCRR to launch the initiative. Delaware received $160,000 to upgrade network infrastructure at Delaware State University and to install a high-memory compute server in the BioIT center at DBI. The remainder of the funds has been awarded to Maine.(4) High-throughput Genomics Research Capability+ A high-throughput genomics research capability is being installed at DBI to significantly upgrade the capabilities of the Network. To meet this objective, a Sequence-by-Synthesis (SBS) instrument based on Solexa's Massively Parallel Signature Sequencing (MPSS') technology has been ordered with funding provided by the NSF-EPSCoR program and a grant from the Unidel Foundation. This 'next-generation' instrument will generate large amounts of short reads (35 to 50 nucleotides) and thus creates significant amounts of data per instrument run. This makes the technology ideal for rapidly and economically developing datasets that can be compared against an existing genomic database or where the potential for chimeric sequence assembly is low. To accommodate this data-influx, a very-high-memory database server, funded through the INBRE Administrative Supplement described above, has been installed in the BioIT Center to provide the bioinformatics pipeline required for data handling and analysis. (5) Collaborative Research Capabilities at the Desktop Level + Despite its small size, there is a growing need in Delaware for improving cyber-based communications among researchers and educators. Polycom-based videoconferencing systems that utilize the H.323 protocol and facilitate classroom-based or group discussions are in place at most of the participating institutions due to an NIHINBRE Supplement awarded in 2005. We plan to build on this base by providing desktop videoconferencing access to individual researchers through H.323-compatible systems such as Ekiga or NetMeeting for PCs, or XMeeting for Mac OSX. Many of these solutions are open-source and require only a camera and microphone at the user level and sufficient bandwidth on the institutional level. In addition, we plan to expand the use of collaboratories that allow researchers to access high-end instrumentation located at core instrumentation centers. The DBI Bioimaging Center already uses Quartz PCI collaborative software on its multi-photon and field emission scanning electron microscopes to provide remote access to these unique and complex instruments for researchers across the State.
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