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2013 UVA Research Data Fair BioConnector

2013 UVA Research Data Fair BioConnector

Slides given at a panel discussion about bioconnector.virginia.edu at the 2013 UVA Research Data Fair.

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Stephen Turner

October 18, 2013
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Transcript

  1. A multi-faceted approach connecting researchers to the resources and services

    they need Stephen D. Turner, Ph.D. Bioinformatics Core Director bioinformatics@virginia.edu Twitter: @genetics_blog Slides available at: stephenturner.us/slides
  2. UVA Bioinformatics Core •  Established Oct, 2011. •  A centralized

    resource for providing expert and timely bioinformatics consulting and data analysis. •  Main goals: help collaborators publish and get funding. –  1. Service –  2. Training –  3. Infrastructure
  3. bioinformatics.virginia.edu/services •  Gene expression: Microarray –  Affymetrix, Illumina, Custom – 

    QA, analysis/visualization, pathway analysis, etc –  Deposit in GEO •  Gene expression: RNA-seq –  Differential gene expression –  Differential isoform expression, exon usage, splicing, etc. –  http://dx.doi.org/10.6084/m9.figshare.105157 •  Pathway analysis –  GO, GSEA, SPIA, IPA, oncomine, ... –  http://dx.doi.org/10.6084/m9.figshare.105155 •  DNA Methylation –  Infinium chips, MeDIP-seq, etc –  http://dx.doi.org/10.6084/m9.figshare.105157 •  DNA Binding / ChIP-Seq –  Peak calling, differential binding •  DNA Variation –  GWAS, NGS •  Metagenomics –  Microbiome –  Microbial forensics •  Acquisition / analysis of public data –  GEO, dbGaP, SRA, ArrayExpress, etc. –  Download and upload •  Grant / Manuscript support –  Letter of support, resources, etc. •  Custom development
  4. A physical and virtual informatics hub for faculty to connect,

    collaborate, and receive research support services Partners: Bioinformatics Core Health Sciences Library Div. Biomedical Informatics
  5. How is new technology changing bioinformatics theory and practice? Data.

    Lots of it.
  6. Bioinformatics Gaps As science becomes increasingly dependent on computation: How

    best to ensure that analyses are reproducible? How can methods best be made accessible to scientists? How to facilitate transparent communication of analyses? A crisis in big data biological research: reproducibility
  7. BioConnector: Bioinformatics galaxy.bioconnector.virginia.edu •  Open, web-based platform for big data

    biological research •  Bioinformatics toolkit •  Workflow management system •  Facilitates transparency, reproducibility, sharing •  Regular workshops in HSL (slides at stephenturner.us/slides) wiki.bioconnector.virginia.edu •  A simple-to-use wiki, aimed at creating documentation. •  75 registered users •  Can be used by service providers (Bioinformatics Core, Clinical Informatics, HSL) to easily document and share data/ methods/results with clients and collaborators.
  8. Informatics tutorials •  New Oct 2013 •  Over 100 tutorial

    suites on informatics resources •  Video lectures, screencasts, handouts, exercises, etc.
  9. Research Navigator •  UVA has many support services distributed across

    grounds. •  Finding the one you need is challenging! à Research Navigator
  10. Clinical Informatics •  Contact: james.harrison@virginia.edu •  MuSIC Research Databases – Rapid

    development of web-based custom research databases for variety of purposes. •  Clinical Data Repository – HIPAA-compliant integrated research database containing de-identified clinical and administrative information on >1M patients and >5M encounters at UVA.
  11. Physical Presence •  Technology-enabled collaborative workspace –  Research-service focus – 

    Videoconferencing –  Floor-to-ceiling whiteboard-painted walls
  12. Collaboration Discovery •  Investigating / in development •  Capture the

    entire scholarly output of University of Virginia –  Enable collaborative team science –  Peer comparison –  Custom reporting •  Benefits to Investigators: –  Discover potential collaborators –  More rapidly and competitively form teams •  Benefits to Administrators: –  Better data for Institutional business intelligence –  Better assess performance for annual reviews
  13. Free Stats Consulting w/ PHS •  Coming soon! •  Gap:

    no-cost baseline statistical/computing/ informatics support. •  Public Health Sciences, in partnership with HSL, will provide free basic statistical and research consulting in the library. •  Also: statlab.library.virginia.edu
  14. Bioinforma)cs  Core   Stephen  Turner,  Ph.D.   bioinforma)cs@virginia.edu   Div.

     Biomedical  Informa)cs   Jim  Harrison,  M.D,  Ph.D.   james.harrison@virginia.edu   Health  Sciences  Library   Gretchen  Arnold,  MLS   Bart  Ragon,  MLS   gvn8r@virginia.edu   bioconnector.virginia.edu Slides  available  at:  stephenturner.us/slides