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. The primary goal of the Bioinformatics Core is to facilitate the analysis and interpretation of various types of data for RI-INBRE-supported investigators at the network institutions. The data types include nucleotide and amino acid sequences, protein domains, and protein structures. Then, by applying informatics, the Bioinformatics Core assists the researchers in understanding and organizing different types of information. A wide variety of software and hardware applications have been acquired by the Bioinformatics Core to assist in the analysis and interpretation of the data. In the future, the core will continue to develop bioinformatics courses, training sessions, lectures, and seminars. Dr. Daniel Udwary, a recently hired specialist in bioinformatics, coordinates the direction and activities of the Core. In the coming year, Dr. Udwary's focus will be to expand the core's outreach and instructional activities in order to increase the usage of the Bioinformatics Core services and software. Additionally, the Bioinformatics Core is currently working with the Northeast Cyberinfrastructure Consortium on an NIH proposal that will greatly enhance the cyberinfrastructure available to researchers throughout the Northeast. Bioinformatics Software: The major bioinformatics software continues to be our molecular modeling software, our GCG bioinformatics software, SeqLab and SeqWeb, and Sequencher. Last year UNIX based Insite II molecular modeling programs were converted 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 two years ago. A dedicated server for the Sequencher license enabled users to log on from various locations. We increased the number of licenses so that all users at the Primarily Undergraduate Institutions (PUIs) that needed Sequencher had access. A stand alone version of the application is deployed at the PUIs where needed. Video Conferencing: A video conferencing network was implemented over the last 18 months. Each of the network institutions received a mobile cart with full video and data conferencing capabilities based on the Polycom VSX7400. Each system contained dual 20"""""""" LCD screens and a mobile camera. All six of the mobile carts are deployed, one at each network institution. Last year, firewall and network issues added to the complexity of the deployment, but these have been resolved. Conferences have been conducted throughout the network and between other INBREs in the Northeast. The core has also initiated broadcasts of the RI-INBRE seminar series allowing for increased participation by the Network institutions. Bioinformatics Classes and Training Session(s): The recent hiring of Dr. Udwary at the University of Rhode Island (URI) expands our offering in bioinformatics. For the eighth consecutive year, a graduate level bioinformatics class was offered at the University of Rhode Island. This year the class was taught by Dr. Udwary, who has 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. Together with Dr. Bethany Jenkins in CELS, Dr. Udwary will develop a new course in undergraduate bioinformatics that is less research oriented and more """"""""hands-on"""""""", this will allow undergraduate students to learn access and most importantly utilize bioinformatics tools. We continue to have workshop sessions. Dr. James Vincent from The Vermont Genetics Institute came to URI and led a discussion as to the types of bioinformatics resources that are available at the VT-INBRE. This was the first of a series of sessions where other bioinformatics core leaders in the area will be brought in and the scope of their operations discussed. In addition, discussions were held with the RI-EPSCOR office concerning bioinformatics. We investigated possible areas of overlap and ways that the RI-INBRE and RI-EPSCOR could collaborate. It was decided that both groups would hold joint bioinformatics seminars which will allow for larger audiences and a greater number of presentations. Outreach Efforts: We 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. One such seminar included a presentation by Dr. Zhong-Yin Zhang from the Indiana University School of Medicine entitled """"""""Chemical Genetic and Proteomic Studies of Protein Tyrosine Phosphatases"""""""". Presentations: In November a poster was presented by the Bioinformatics Core at the 3rd Annual Biology New England South (BioNES) meeting at Roger Williams University on December 2, 2008. In addition, a poster focusing on RI-INBRE bioinformatics tools and resources was presented at the RI-INBRE Research Fellows Meeting and Faculty Retreat at Roger Williams University in Bristol, RI on January 30, 2009. At that meeting, RI-INBRE-supported investigators were polled as to their bioinformatics needs and usage. The RI-INBRE Bioinformatics Core was also a participant and presenter at the Cyber infrastructure Workshop held at the NIH, NCRR 2nd Biennial IDeA Symposium of Biomedical Research Excellence (NISBRE) in Washington, DC on August 6-8, 2008. Dr. Udwary also promoted the bioinformatics core by presenting various seminars including """"""""Secondary metabolic gene clusters from the genome of the marine actinomycete, Salinispora arenicola CNS-205"""""""" and """"""""Biosynthesis of cyclomarin, an anti-inflammatory cyclic heptapeptide produced by Salinispora arenicola"""""""" at the Gordon Conference on Marine Natural Products in Ventura, CA on February 24-29, 2008, """"""""Accessing genomic data for the prediction and elucidation of actinomycete natural product chemical structures"""""""" at the Department of Chemistry, Brown University on April 8, 2008, and """"""""Chemical genetics: Examples from the marine actinomycete genus, Salinispora"""""""" during the Interdisciplinary Research Seminar Series at the University of Rhode Island on March 7, 2008. Summary: Throughout 2008, education and updating of bioinformatics software has significantly increased the volume and depth of usage of all aspects of our bioinformatics core. As a result of the increased usage, eight publications in the last year have acknowledged use of the RI-INBRE Bioinformatics Core Facility. In addition the RI-INBRE Bioinformatics Core was a participant in the Northeast Network Initiative (NENI) to advance cyber infrastructure throughout the northeast. The core was also a participant in the EPSCoR Track II proposal that will further expand cyberinfrastructure in the Northeast if funded. A similar INBRE proposal for enhancing cyberinfrastructure in the Northeast, including RI, will be submitted on March 1, 2009.
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