VERMONT 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. VGN Bioinformatics Core Highlights June 2008  June 2009 Bryan Fleming Julie Dragon James Vincent General Highlights Julie Dragon, Ph.D. was hired as Research Analyst. Dr. Dragon will work with Jeff Bond in the Microarray Facility performing microarray analyses. A Shared Instrumentation Grant has been submitted (Vincent, P.I.) to NCRR for acquisition of a Next Generation Sequencer (Illumina Genome Analyzer). If funded a next generation facility will be implemented that will significantly enhance the research capabilities provided by VGN to UVM and BPI researchers. Julie Dragon - Research Analyst Database Development (with Jeff, Rama, Tim, Scott) Implemented a database for logging activities, tracking project status, and connecting investigators to projects, funding streams, and publications Planned the transfer of this database to the Biodesktop in the next few months Developed new microarray forms and determined the best way to track orders and serve data; this too will be applied through the Biodesktop in the near future Data Analysis Training Shadowed Jeff on consultations with microarray users in order to become familiar with project design, the analysis pipeline, and quality control Attended Affymetrix University workshop in London Participated in a webinar with the creator of XRAY, a program designed to analyze gene/exon arrays, and I have since taken the lead on the analysis of these arrays Participated in two workshops with Jeff, 1) on the excel output of the pipeline analysis with folks at Maine Medical, and 2) the use of Ingenuity IPA to place that output into a biological context with Ralph Budd and others Jeff and I continue to develop a relationship with investigators and Maine Medical, and have been invited to give a seminar there in the coming months Research Analyst project tracking Development: 48% Training: 36% Research: 16% Bryan Fleming - Administrative IT Core Facilities Database VGN Core Facilities Database upgraded  191 Facilities Total Search results now mapped, international cores supported Outreach Migrated the LMS (learning management system) migrated to new server Worked with ETS to implement an imaging process for laptops - Restoring a laptop to a pristine state now takes 10-20 minutes. Refined gel scanning process for proteomics outreach. Other Rebuilt ERIS to batches emails. Send takes 20 seconds instead of 10-20 minutes. Submitted essays for CSSLP (Certified Secure Software Lifecycle Programmer) certification Upgraded applications PDF processing program. Polycom Bridge operational Surveys sent out & reminders - all but two have completed. Implemented wireless connection for 80 Colchester to campus Distribution of 112 out of 191 facilities tracked in VGN Core Facilities Database affiliated with an association or program. NICL: 13% Cancer Center: 13% INBRE: 10% COBRE: 8% CTSA: 2% NERTRN: 5% EPSCoR: 4% James Vincent - Director Research Classification of variants with Marc Greenblatt Continued work on EPSCoR STREAMs project Minor support for several people (BLAST analysis, scripts, etc) Grants Writing Aim1 of Challenge Grant for project with Greenblatt Submitted Shared Instrumentation Grant for Illumina Genome Analyzer Contributing to research plans for ARRA supplement requests Planning stages for NSF grant with VACC on cloud computing  with Wang, Devins Meetings Clinical and Translational Informatics Networking Meeting  Arizona (Tim,Rama) ABRF  Memphis Service VACC Research Committee  planning future usage policies and capacity VACC Technical Committee  planning future hardware needs VACC  implemented network login for Visualization Lab EPSCoR IT position hiring committee + Panelist (2008) Science Career Panel, Career Day, Vermont Genetics Network, Burlington, VT + Presenter (2008) National IDeA States of Biomedical Research Excellence, Core Technology Breakout Session, August 2008, Washington DC + Panelist (2008) Northeast Regional Life Sciences Core Directors Meeting, Oct. 2008, Burlington, VT, "Bioinformatics/Computational Biology" + Presenter (2009) Clinical Translational Informatics Meeting, Feb. 2009, "Leveraging Regional and National Resources through Tools, Networks, and Forums", Scottsdale, AZ + Attended (2009) Network of IDeA-funded Core Laboratories Satellite Workshop Meeting, co-organizer. Feb. 2009, Memphis, TN + Seminar Directing A Bioinformatics Core (2008) College of Pharmacy, University of Rhode Island, Kingston, RI