Conference Program - ABRF 2011 - Association of Biomolecular ...

(W13) Institutional Core ManagementS. Meyn 1 , P. Turpen 2 , G.K. Farber 3 , S. Mische 4 ,P. Alexander 5 , J. Auger 61Vanderbilt University Medical Center, Nashville, TN, UnitedStates; 2 University of Nebraska Medical Center, Omaha,NE, United States; 3 National Center for Research Resources,Bethesda, MD, United States; 4 New York University LangoneMedical Center, New York, NY, United States; 5 MorehouseSchool of Medicine, Atlanta, GA, United States; 6 University ofCalifornia San Francisco, San Francisco, CA, United StatesThis workshop session will focus on issues related to InstitutionalCore Management, in response to the national conversation evolvingaround research core facility issues and management. The workshopwill be formatted as an experts’ panel; each participant currentlyplays an important role in supporting and developing research coreresources at an institutional level. Some of the topics to be discussedinclude: (1) Core Consolidation — one size fits all? (2) Bottom-up vs.top-down management, advantages and disadvantages of centrallymanaged cores. (3) Performance metrics and impacts on professionaldevelopment, core infrastructure support and improved operations.(4) Impacts of NIH-NCRR programs on improving access to researchresources, including core facilities. We also plan to highlight the newCore Administrators Network Coordinating (CAN). In responseto an emerging trend to centralize the oversight of research corefacilities, ABRF has fostered development of this network and anew committee: the Core Administrators Network-CoordinatingCommittee (CAN-CC). The committee seeks input and participationfrom scientists, administrators and others with an interest in issuesrelated to the administration of research core facilities which, by thenature of their service role, must interface with multiple constituencieswithin a research enterprise. Today many institutions have establishedadministrative positions designed to assist core facilities withmanagement of economic, regulatory and performance issues. In orderto facilitate greater interaction between and among core scientistsand administrators, the mission of the CAN-CC is to contribute to thecommon interests of core administrators, and promote interactions withcore scientists in a collegial and productive manner. The specific goalsof the Core Administrators Network Coordinating Committee (CAN-CC) are: to identify and reach out to our target community; provideopportunities for networking; and assess goals for program focus anddevelopment.(W14) Next Generation Sequencing Softwarefor Data Management, Analysis, andVisualization(W14-1) Tools for Next Generation Sequencing DataAnalysisK. BodiTufts University School of Medicine, Tufts University CoreFacility, Boston, MA, United StatesAs NGS technology continues to improve, the amount of data generatedper run grows exponentially. Unfortunately, the primary bottleneckin NGS studies is still bioinformatics analysis. Not all researchershave access to a bioinformatics core or dedicated bioinformatician.Additionally, much of the software for NGS analyses is written to runin a Unix / Linux environment. Researchers unfamiliar with the Unixcommand line may be unable to use these tools, or face a steep learningcurve in trying to do so. Commercial packages exist, such as the CLCGenomics Workbench, DNANexus, and GenomeQuest. However,these commercial packages often incorporate proprietary algorithmsto perform data analysis and may be costly. Galaxy provides a solutionto this problem by incorporating popular open-source and communitylinux command line tools into an easy to use web-based environment.After sequence data has been uploaded and mapped, there are avariety of workflows for NGS analyses that use open-source tools. Thisincludes peak-calling analyses for ChIP-Seq (MACS, GeneTrack indexer,Peak predictor), RNA-Seq (Tophat, Cufflinks), and finding smallinsertions, deletions, and SNPs using SAMtools. Any researcher canapply a workflow to his NGS data and retrieve results, without having tointeract with a command line. Additionally, since Galaxy is cloud-based,expensive computing hardware for performing analyses is not needed.In this presentation we will provide an overview of two popular opensourceRNA-Seq analysis tools, Tophat and Cufflinks, and demonstratehow they can be used in Galaxy.(W14-2) GenomeView: Visualizing the Next-Generation of DataT. AbeelBroad Institute of MIT and Harvard, Cambridge, MA, UnitedStates, and VIB Department of Plant Systems Biology, GhentUniversity, Ghent, BelgiumDue to recent advances in sequencing technologies, billions of nucleotidesequences are now produced on a daily basis. A major challenge isto visualize these data, including both whole genome sequence andtranscriptome data, for further downstream analyses. Visualization isoften overlooked and undervalued, but it is an extremely valuable toexplore your data on several levels. A first area where visualization shinesis at the early stages of data analysis to perform sanity checks on yourdata. Eye-balling your data in a visually pleasing way is the best way toget a good feel on what came out of your experiments. Once you havea good idea of what is in your data a good visual representation can beused to generate new hypotheses and to fine-tune analysis parameters.The appropriate image often makes the solution obvious and as such, itreally makes it easier to develop algorithms. The ability to interactivelyexplore gives you insights in large-scale data sets and definitelyaugments our ability to reason about complex data. To this end, wepresent GenomeView, a stand-alone sequence browser specificallydesigned to visualize and manipulate a multitude of genomics data.GenomeView enables users to dynamically browse high volumes ofaligned short read data, with dynamic navigation and semantic zooming,from the whole genome level to the single nucleotide. At the same time,the tool enables visualization of whole genome alignments of dozens ofgenomes relative to a reference sequence. GenomeView is unique in itscapability to interactively handle huge data sets consisting of dozensof aligned genomes, thousands of annotation features and millions ofmapped short reads both as viewer and editor. GenomeView is freelyavailable for academic use as an open source software package athttp://genomeview.org.Workshop SessionAbstractsABRF 2011 — Technologies to Enable Personalized Medicine • 51