A multi-faceted approach connecting researchers to the resources and services they need Stephen D. Turner, Ph.D. Bioinformatics Core Director [email protected] Twitter: @genetics_blog Slides available at: stephenturner.us/slides

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

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

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

How is new technology changing bioinformatics theory and practice? Data. Lots of it.

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

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.

Informatics tutorials •  New Oct 2013 •  Over 100 tutorial suites on informatics resources •  Video lectures, screencasts, handouts, exercises, etc.

Research Navigator •  UVA has many support services distributed across grounds. •  Finding the one you need is challenging! à Research Navigator

Clinical Informatics •  Contact: [email protected] •  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.

Physical Presence •  Technology-enabled collaborative workspace –  Research-service focus –  Videoconferencing –  Floor-to-ceiling whiteboard-painted walls

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

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

Bioinforma)cs  Core   Stephen  Turner,  Ph.D.   bioinforma)[email protected]   Div.  Biomedical  Informa)cs   Jim  Harrison,  M.D,  Ph.D.   [email protected]   Health  Sciences  Library   Gretchen  Arnold,  MLS   Bart  Ragon,  MLS   [email protected]   bioconnector.virginia.edu Slides  available  at:  stephenturner.us/slides