1. Bioinformatics in Libraries: building new services from the ground up at UC San Francisco Megan Laurance, Ph.D. Research Informationist UCSF Library and Center for Knowledge Management

2. Research Support @ UCSF Library Information Resources Classes Online Guides Consultation with subject experts in the Library

3. Research Informationist Role at UCSF Hired February 2013 Ph.D. in Molecular and Cellular Biology with background in knowledge management, data curation, genomics Bioinformatics Services for Biologists –Focus on databases, analysis tools that are accessible to biologists without programming experience Data Management Services –Early stages, focus on data sharing, data repositories Embedded on 2 research projects –Providing both data management and bioinformatics services

4. Bioinformatics Resources for Biologists One-on-one consultation and monthly workshops on various resources

5. Ingenuity Pathway Analysis Services Genomic data analysis tool available to all researchers at UCSF Operates on a re-charge model, like a core lab Hands-on training classes every other month Drop-in clinic at the end of class for researchers with specific questions Consultation (hourly fee) on data analysis

6. Bioinformatics Resources for Biologists Workshop Series Launched in Fall 2013 Introduction to Methods in Pathway Analysis Introduction to Genomic Data Repositories and Analysis Resources IPA (Ingenuity Pathway Analysis) Training Cytoscape 3.0 Training. Instructor: Alex Pico, Gladstone Institutes Bioinformatics Core UCSC Genome Browser Seminar. Instructor: Bob Kuhn, UC Santa Cruz Gene Set Enrichment Analysis. Instructor: Matthew Gormley, Fisher Lab, UCSF Introduction to Human Genetic Variant Databases Coming Soon: The Cancer Genome Atlas (TCGA)

7. Bioinformatics Workshops: Publicity, Registration E-mail blast to a list of >400 researchers Post-doc listserv Flyering: it’s old school, but it works Register through Library Class Calendar

8. Example: Content of Genomic Data Repositories Workshop 90-minute workshop 45-minute lecture-style introduction Research Data Repository Landscape and Ecosystem Why Share Data? Sometimes you have to… Why Share Data? It’s good for science & scientists Why reuse public datasets? Use Cases! Examples! Deep dive on one genomic data repository: NCBI Gene Expression Omnibus (GEO) 45-minute hands on data reuse exercise

9. Example: Content of Genomic Data Repositories Workshop 45-minute hands-on exercise in data reuse: Real-world use case: search, analyze, mine for knowledge

10. Bioinformatics Workshop Series: by the numbers Registration and turnout has been very good. Registrants are then added to our e-mail distribution list, which is continually updated

11. Bioinformatics Workshop Series: who attends? Postdocs biggest group Faculty, although smallest in number, provide greatest exposure, new opportunities

12. Outcomes: are these workshops valuable to attendees? Very positive feedback overall Aspects that attendees found most valuable: –Awareness of methods, databases, software tools for genomic data –Hands-on practice with the repositories, tools, based on real world use cases –Links to resources including forums, tutorials, campus experts

13. Outcomes: attendees’ suggestions for improving the workshops More time for hands-on exercises Divide workshops into dedicated “deep-dive” workshops on a single topic (rather than intro or survey of many) Offer it again to get more practice

14. Outcomes: New Opportunities Collaboration with postdoc in pharmacogenomics lab –Data re-use case: analysis of public genomic data to confirm, inform novel findings from their proprietary data –Co-author on 2 posters Invited to teach 2 classes in the Biomedical Sciences Graduate Program –Winter quarter mini-course on “Getting Comfortable with Big Data” –37 1 st year Ph.D. students –Will repeat for new Ph.D. students this Fall Office Hours/Consultations with students, postdocs, faculty –How do I find and analyze data from my area of interest? –Data Sharing Plan requests – coming from faculty who attend genomic data repository workshops

15. Outcomes: More New Opportunities Next Generation Sequencing Data Analysis Software “Bake-Off” –Coordinated multi-vendor evaluation for Genomic Medicine Initiative and Institute for Human Genetics UCSF Clinical Exome, Variant Database –Data curation, data management –Evaluate phenotype ontology tools for documenting patient phenotype at point of care

16. Next steps Keep the momentum going on the workshop series: –Partner with our Graduate Division to line up postdocs to teach workshops –Partner with other campuses in the University of California system –Nurture relationships with faculty to enable more integration into curriculum –Developing “Genomic Data Repositories and Analysis Tools” into CE course for MLA 2014, Austin, TX Address growing need/demand for training in programming languages: –R, Perl, Python Software Carpentry Bootcamp Facilitate meet-ups in the Library’s new collaboration space

17. Acknowledgements Karen Butter, University Librarian and Assistant Vice Chancellor, UCSF Julia Kochi, Director, Collections and User Services, UCSF Library

18. Thanks! Questions? megan.laurance@ucsf.edu I’m happy to share content, exercises, and links to resources from the workshop.