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.Bioinformatics Programs: The major update of bioinformatics software was the conversion of all of our UNIX based Insite II molecular modeling programs to Accelrys's PC based Discovery Studio. A new Dell workstation was purchased so that these programs would run efficiently. Sequencher a powerful, user-friendly DNA sequence assembly and analysis software that results in high quality, reliable DNA contigs was added last year. A dedicated server for the Sequencher license enables users to log on from various locations and an increase in the number of licenses is planned to allow for simultaneous users. A PC based version of the application is being considered as an alternative.Video Conferencing: As part of the RI-INBRE RFA supplement, a video and conferencing network was proposed. The video conferencing network was implemented over the past year. Each of the network institutions received a mobile cart with full video and data conferencing capacity based on the Polycom VSX7400. Each system contained dual 20' LCD screens and a mobile camera. This particular arrangement allowed greater flexibility. In conference mode, each site sees the individual speaking on one screen while the other screen displays a split image of all the conference participants. The conference participants also have the ability to produce or edit documents in real time. In seminar mode, one screen shows the seminar speaker and the other screen displays the PowerPoint presentation. Each mobile cart also has the ability to connect to a digital projector so that seminar speakers and their PowerPoint presentations can be viewed by a larger audience on screens in auditoriums, lecture halls, etc.Presently all six of the mobile carts are deployed at their respective sites. Firewall/network issues have added to the complexity of the deployment but in large part these have been resolved. Conferences have been conducted throughout the RI-INBRE network and between other INBREs throughout the Northeast and we have initiated broadcasts of the RI-INBRE seminar series allowing for increased participation by the Network institutions.Bioinformatics Class / Training Session(s): For the seventh consecutive year, a graduate level bioinformatics class was offered at the University of Rhode Island. This class initiated research projects that resulted in collaborations among faculty from varied disciplines in informatics and the biological sciences. Student projects were especially successful with many continuing as directed studies and MS thesis topics. In addition to graduate thesis topics, further increases in bioinformatics software usage among summer students led to summer projects where the discipline of bioinformatics played a more centralized role in student projects. As we approach the summer of 2008, we expect future summer projects to continue this positive development. The recent hiring of Dr. Daniel Udwary at the University of Rhode Island will expand our expertise in bioinformatics. He will teach an undergraduate bioinformatics class that is less research oriented and more 'hands-on', will allow undergraduate students to learn, access and most importantly utilize bioinformatics tools.We continue to have high quality workshops and training. The most recent workshop and training session took place on February 5, 2008 with Dr. Vladimir Brusic, the director of Bioinformatics at the Cancer Vaccine Center of the Dana-Farber Cancer Institute. Dr. Brusic conducted a workshop and training session entitled 'Bioinformatics Applications for Analysis of Viruses and Cancer Antigens'. We plan to continue similar training events throughout the year. Outreach Efforts: Efforts continue to develop a formal relationship with the Community College of Rhode Island (CCRI) to provide CCRI faculty with training and access to bioinformatics software. Faculty members at CCRI have begun utilizing available bioinformatics tools and integrating such material into existing courses. This relationship has allowed CCRI faculty to introduce their students to bioinformatics and will continue to enhance the laboratory experience for CCRI students. The RI-INBRE investigators at the primarily undergraduate institutions were granted access to the electronic library resources at the University of Rhode Island last year. This has greatly increased their access to electronic journals. Additional outreach efforts include bioinformatics seminars which are open to all interested parties. Recent seminars include a presentation on October 18, 2007 by Dr. Daniel Udwary from The Scripps Institute, University of California, San Diego, entitled, 'The Bioinformatics of Chemistry: Natural Product Pathways in Plant Symbiont Microbes' as well as a presentation on December 4, 2007 by Dr. Elgar Pichler from the Scientific Information Services, Discovery Information, AstraZeneca R&D, Boston, MA entitled, 'Through the Looking Glass: The Nuclear Receptor Dimerization Network'. Exposure/Presentation: In March 2007 RI-INBRE a poster focusing on RI-INBRE bioinformatics tools and resources was presented at the New Mexico Bioinformatics Symposium. In September 2007, research entitled PFAST: protein fluorescence and structural toolkit, was presented at the XIIth European Conference on the Spectroscopy of Biological Molecules, Bobigny, France. RI-INBRE was also a participant and presenter at the Cyberinfrastructure Workshop held at the Northeast IDeA meeting in Burlington, VT on August 15-17.Summary: Throughout 2007, the intensive training, education and updating of bioinformatics software has significantly increased the volume and depth of usage of all aspects of our bioinformatics core. We anticipate even more growth during 2008. In addition RI-INBRE Bioinformatics Core was a participant in the NENI consortium to advance cyberinfrastucture throughout the northeast. An INBRE Administrative Supplement for enhancing cyber infrastructure in RI was submitted to NCRR, but not funded.Future Directions: Training sessions, lectures and further outreach opportunities will be continued with the primary goal of increasing the use of the bioinformatics software package(s). Daniel Udwary, a recently hired specialist in bioinformatics will coordinate the direction and activities of the Core. We will continue to work with NENI to expand out cyber infrastructure.
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