bioinformatics in libraries: building new services from the ground up at uc san francisco megan...
TRANSCRIPT
Bioinformatics in Libraries: building new services from the ground up at UC San Francisco
Megan Laurance, Ph.D.Research InformationistUCSF Library and Center for Knowledge Management
Research Support @ UCSF Library
Information Resources Classes Online Guides Consultation with subject experts in the Library
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
Bioinformatics Resources for Biologists
One-on-one consultation and monthly workshops on various resources
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
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)
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
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
Example: Content of Genomic Data Repositories Workshop
45-minute hands-on exercise in data reuse: Real-world use case: search, analyze, mine for knowledge
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
Bioinformatics Workshop Series: who attends?
Postdocs biggest group Faculty, although smallest
in number, provide greatest exposure, new opportunities
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
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
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 1st 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
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
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
Acknowledgements
Karen Butter, University Librarian and Assistant Vice Chancellor, UCSF
Julia Kochi, Director, Collections and User Services, UCSF Library
Thanks! Questions?
I’m happy to share content, exercises, and links to resources from the workshop.