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 Research Instrumentation Core The core instrumentation centers, partially supported by INBRE funding, play a critical and enabling role to facilitate life-sciences-based research across Delaware. Many of the core centers are located at the Delaware Biotechnology Institute (DBI) and at selected departments within the University of Delaware (UD). Special consideration is placed on securing equal access for faculty and students at any of the partner institutions in the statewide INBRE Network. All of Delaware's researchers are less than two-hour travel distance from the core centers, and high-speed internet connectivity enables remote desktop access to the bioinformatics center and to the bioimaging facilities, where several collaboratories have been employed to enable internet-based access to microscopy resources. The core centers can be easily accessed through a dedicated web portal under www.dbi.udel.edu/coreinstrumentation.html. At this site, detailed information is provided with web-based instrument descriptions, on-line reservation calendars, billing and assessment tools to optimize access and use of these resources. The core center network includes the Biomolecular Core Center located at Nemours Biomedical Research, a part of the A.I. Hospital for Children, complementing the existing six centers in Bioimaging, Bioinformatics, DNA Sequencing &Genotyping, Structural Biology &NMR, Proteomics &Mass Spec, and Protein Production &Characterization. The INBRE program provided support the Core Instrumentation Centers through the following four mechanisms: 1) Instrumentation upgrades to support the research goals of the ?details are provided below;2) Partial salary support for Core Center staff to ensure the professional operation of the instruments ?during Year 4 of the INBRE, this support comprised 40% each for 7 core center staff members;3) Instrumentation maintenance in the amount of $28,000;and 4) Core Center Fee Waivers in the amount of $17,000 for faculty and students in the INBRE partnership to allow them to use the core centers for free to obtain initial data and provide startup-support for new scientific ideas. Investments: In 2007, the Core Centers have received instrumentation upgrades that were funded by a variety of sources. This is an indication that some of the initial INBRE investments into the Core Centers are beginning to translate into success with attracting other funding sources, paving the way toward long-term sustainable core centers. The most significant installations are listed below: 1) Zeiss LSM 5 DUO high-speed confocal imaging system ($785,000) The new confocal imaging system, that has been installed in the Bioimaging Center, will increase the speed of imaging by up to 100-fold over current microscopes. This new system will be applicable to a wide array of life science and materials engineering research, including high resolution motion analysis, photo manipulation of cells or materials, molecular interactions, physiological interactions, small particle diffusion and particle tracking in cells and materials, four-dimensional imaging, and spectral imaging. More than 20 researchers have identified an immediate use for this new system. Zeiss demonstrated the system in the spring during a regional users workshop at DBI. Following the workshop the unit remained at DBI for 3 months, where it was used for more the 560 hours confirming the value of this new capability. Funding for this instrument is provided by the Unidel Foundation ($500k), several UD departments, and the Delaware Biotechnology Institute ($288k). 2) Illumina Sequencing-by-Synthesis (SBS) Machine ($625,000) A """"""""next-generation"""""""" high-throughput sequencing instrument will be the cornerstone of a significantly expanded DNA sequencing facility to support the research and development of novel applications. In addition, due to the magnitude of the data generated by this instrument, additional computer hardware has been recently installed in the Bioinformatics Center (see Sunfire Bioinformatics upgrade described above) for the development of a bioinformatics pipeline required for data handling and analysis. The SBS instrument promises to revolutionize not only the amount of sequence produced per unit time, but the ease of use and breadth of the application of ultra-high throughput sequencing. This advanced sequencing technology frees the user of traditional cloning techniques, in the process eliminating most of the bias, cost, and labor associated with traditional DNA sequencing. The SBS instrument provides a large number of short reads (35 to 50 nucleotides) and generates a significant amount 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. Members of the UD user group already are exploiting the strengths of both technologies and the establishment of this instrument will drive further innovation and application development, as well as pulling in new users from across campus and the region. Partial funding for this instrument will be provided by the EPSCoR RII program ($250k) with significant matching contributions ($375k) expected from the Unidel Foundation. The final decision on the Unidel proposal is expected in December 2007. 3) SunFire X4600 M2 8-Node Database Server ($64,000) With the need to process progressively larger genomic calculations (Blast, Massively Parallel Signature Sequencing/MPSS, Sequencing-by-Synthesis, etc.), the amount of accessible core memory on the compute servers necessary to return results in a timely fashion has been growing exponentially. These types of calculations are generally limited by the bottleneck in memory usage, and turn-around time can be drastically decreased by added memory. The compute server in the Bioinformatics Center currently consists of 120 dual-core/2GB ram systems, seven quad-core/8GB systems, and six quad-core/16GB systems. While the current systems were more than adequate when they were first installed in 2003, the current processes and databases will require at least 32GB ram and could grow to more than 64GB within a few months. Therefore, the best solution to meet the growing demand is to include one or more very-large-memory systems in the grid infrastructure. The Sun Microsystems SunFire X4600M2 server fits these requirements and is compatible with the current grid hardware. Funding for this upgrade has been secured through a supplemental cyberinfrastructure grant under the INBRE program that was awarded in October 2007. 4) Upgrade of Network Infrastructure at Delaware State University ($100,000) Under the INBRE program, DSU has significantly upgraded its broadband access by teaming with the University of Delaware (UD) for a reduced rate in joining the Internet2 consortium through the Mid-Atlantic Gigapop in Philadelphia (MAGPI) into the Abilene backbone. At this time, the Internet2 link is connected to the DSU Campus, but DSU requires additional resources to link faculty and research labs to this capability. DSU is now in the process of redesigning and modernizing the network infrastructure in the Mishoe Science Center Complex and committed to upgrading and modernizing the network infrastructure in the College of Mathematics, Natural Sciences and Technology. The goal of this expansion is to create a modern, high-performance, robust, and intelligently managed network that can be utilized for research, research training and education and would enable DSU to take full advantage of the Internet2 connectivity. The college consists of the departments of Biology, Chemistry, Computer and Information Sciences, Mathematics, and Physics and Pre-Engineering. All of the departments, except for Mathematics, are housed in the Mishoe Science Center Complex. DSU intends to advance the high bandwidth expansion project by acquiring several 10 GB capable managed switches and supervisor engines to complete the 10 GB network backbone, a security module to secure the network, and the remaining line cards needed for gigabit connectivity to the desktop. Funding for this upgrade has been secured through a supplemental cyberinfrastructure grant under the INBRE program that was awarded in October 2007. Workshops and Seminars: The core center directors meet on a bi-monthly basis to discuss strategies for broadening the interest and user base among Delaware's research community. Core Center Staff participate in regional and national conferences to ensure that their expertise remains up-to-date. A list of these seminars and workshops is attached as Table 1. Seminars, Workshops &Other Core Center Activities Event Location, Dates Core Center Personnel involved Core Center Open House ?Overview and Tours Newark, DE, Oct 5, 07 All Core Center Directors Regional Mid-Atlantic Zeiss LSM confocal microscopy user course/meeting Newark, DE, Jan 16-18, 07 All Bioimaging Center Personnel Zeiss Advanced Confocal Workshop Thornwood, NJ, Oct 07 Kirk Czymmek Advanced Field Emission Scanning Electron Microscopy Workshop Rockville, MD Nov 07 Kirk Czymmek Delaware Membrane Protein Symposium Newark, DE Oct 9, 07 Liz Adams Asylum Research UK AFM Forum Oxford, UK April 16-17, 07 Liz Adams AFM Biomed Meeting Barcelona, Spain, April 19-21, 07 Liz Adams SLB/IEIIS Conference San Antonio, TX Nov 9-11, 06 Liz Adams 2nd Northeast Regional IDeA Meeting Burlington VT, Aug 15-17, 07 Bruce Kingham, Katia Sol-Church Northeast Regional Life Sciences Core Directors (NERLSCD) meeting Ithaca, NY Nov 7-9, 07 Katia Sol Church, Doug O'Neal, Bruce Kingham Association of Biomolecular Resource Facilities (ABRF) 2007 Tampa, FL, March 31- April 3, 07 Katia Sol-Church, Bruce Kingham 1st Annual Nemours Research Core Open House 2006 Wilmington, DE, Oct 23, 07 Katia Sol-Church Analytical Ultracentrifugation Workshop Bethesda, MD, Feb 5-8, 07 Yu-Sung Wu Bruker NMR Users Meeting Princeton, NJ Oct 22-23, 07 Steve Bai Fourier Transform Mass Spectrometry Workshop Indianapolis, IN Jun 2-3, 07 John Dykins American Society for Mass Spectrometry Indianapolis, IN Jun 4-8, 07 John Dykins On October 5, 2007, the third Annual Core Center Open House was held at DBI. This event featured presentations by all of the core center directors, discussing capabilities and included optional tours to the core centers. It attracted 33 faculty and student researchers from across the Delaware INBRE network. In addition, nine members of Delaware's life science industry attended the Open House to learn about the existing capabilities. Based on the evaluations from the Open House, which were overwhelmingly favorable, but with a slight preference given for the core center tours over the initial overviews presented by the core directors, we anticipate very minor adjustments for next year's event. Just as in the previous year, the open house presentations were video-streamed live to all of the participating institutions and are available on-line as streaming Quicktime movies on the DBI core center web site - www.dbi.udel.edu/coreinstrumentation.html. In addition, core centers organize individual workshops and seminars related to their respective instrumentation for the broad research community and are frequently featured during DBI visits by students and teacher groups and help inform and excite the public about the capabilities available to life scientists. + The Regional Mid-Atlantic Zeiss LSM confocal microscopy user course/meeting was held January 16-18, 2007 at DBI's Bioimaging Center. The event attracted over 85 participants representing bioimaging center users from across the Mid-Atlantic Region, including some 60 INBRE-affiliated users from Delaware. The 2-day course was designed to provide training in confocal microscopy for all levels of users. The training, conducted by Zeiss advanced imaging specialists, was split between lecture times and hands-on sessions in the Bioimaging Core Center. The event was video-streamed and can be viewed today on the DBI web server under www.dbi.udel.edu/events/otherVideo.html. + The 2nd Northeast Regional IDeA Meeting was hosted by the Vermont Genetics Network at the University of Vermont in Burlington, VT on August 15-17, 2007. Delaware was well represented at this meeting. Dr. Karl Steiner, Program Coordinator of the Delaware INBRE served as Session Chair for the Computational Biology session, Dr. Abraham Lenhoff, Director of one Delaware's four COBRE programs and Co-Chair of the Core Center Activities in the INBRE, served as Session Chair for the Protein Structure and Function session, and Bruce Kingham, Director of the Sequencing and Genotyping Core Center served as Co-Chair for the Core Facility Workshop, """"""""Developing Best Practices."""""""" In addition, Dr. Karl Steiner organized and moderated a Cyber-Infrastructure Workshop during this event. Additional details can be found on the web under www.uvm.edu/~vgn/. + Several Delaware Core Center Directors helped organize this year's Northeast Regional Life Sciences Core Directors (NERLSCD) meeting, November 7-9, 2007, at Cornell(University in Ithaca, NY (nerlscd.biotech.cornell.edu/). Dr. Katia Sol-Church, Director of the Biomolecular Core at Nemours'Center for Pediatric Research, served as one of the organizers, and Dr. Douglas O'Neal, Manager of the Bioinformatics Center, served as a panel member on the Bioinformatics Panel. Also in attendance was Bruce Kingham, Director of the Sequencing and Genotyping Center. This regional conference attracted 137 registered participants and was co-sponsored by the Delaware EPSCoR, Delaware INBRE, the Delaware Biotechnology Institute and Nemours. Core Center Utilization: the Core Center Directors keep close track of instrumentation utilization and of their user base to evaluate trends and help strategic planning efforts. The INBRE RII leadership realizes the critical value that state-of-the-art instrumentation centers play in conducting innovative research, providing educational opportunities and as recruiting tools to attract the best new faculty and students. As indicated by the usage numbers listed in Table 2, the core centers have seen significant and sustainable growth since last year. This is evident by the increase in both the number of hours and the number of users. In some cases the increase has led to bottlenecks due to popularity of the several centers, especially the Bioimaging Center. Therefore, the decision was made to add an additional staff person, Ms. Shanon Modla, and David Scheiblein as a graduate student helper to the Bioimaging Center staff in 2007. The decline in the use of the Analytical Ultracentrifuge is primarily due to the graduation of 2 major student users. This is counterbalanced by an increase in training for new, incoming students to this core facility that will begin using the instrument in the future. Table 2 ?Core Center Usage Analysis Core Center Valuator 2006 Use 2007 Use Increase [%] Notes Bioimaging # Hours 11,532 12733 10% Sustained Growth Kirk Czymmek # Users 162 204 26% # Faculty 53 67 26% # Depts 15 15 0% DNA Sequencing &Genotyping Bruce Kingham # Samples 10,022 11,119 11% Sustained Growth # Users 158 170 8% # Faculty 42 54 29% # Depts 16 16 0% Bioinformatics Doug O'Neal #CPU Hours 334,623 380,593 14% Sustained Growth #Accounts 14 16 14% #Research Groups 12 10 -17% #Database Groups 4 4 0% #Viz Groups 4 4 0% #Web Sites 8 16 100% #Email Accounts 72 113 57% Protein Production &Characterization Yu-Sung Wu (Analytical Ultra- Centrifuge) #Days 295 132 -55% 2 Major Student Users Graduated #Users 11 11 0% #Faculty 6 6 0% Training Hrs 10 18 75% New Faculty / Students trained #Users 4 7 75% #Faculty 3 7 133% Mass Spectroscopy John Dykins #Weeks 84 84 0% No Change to '06 #Faculty 17 17 0% #Depts 5 5 0% NMR Steve Bai #Samples 27,000 28,000 4% Sustained Growth #Users 83 94 13% #Faculty 28 32 14% #Depts 8 8 0% It should be noted that DBI made the decision in 2007 to close down the Custom Microarray Center due to a lack of interest and patronage among the Delaware INBRE community. Several of the instruments, including the Affymetrix GeneChip system, the GenePix Slide Scanner, and some smaller instruments, remain available for self-use. However, the large-scale robotic systems for making custom microarrays will be sold. One of the key features of the INBRE program is the opportunity for Delaware researchers to request Core Center Fee Waivers. Faculty are invited to submit a short proposal to the RII leadership outlining the core services required, the time period, the estimated cost, and the path forward to secure external funding. In Year 4 to date (7 months into the year), 6 fee waiver proposals have been selected for a total value of $17,000 to be covered by the INBRE grant. This compares to 12 proposals funded for a total value of $30,000 in Year 3. These small grants enable faculty and students across the Network to try out new ideas free of charge and to generate preliminary data to support future research proposals.
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