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We are happy to announce the 2013 Bioinformatics Short Course, to be held 9am-5pm September 16-20, 2013 on the UC Davis campus in Davis, California. This will be our 6th year offering our Bioinformatics Short Course, covering Next Generation sequencing and applications, including:

  • sequencing technologies

  • read quality assessment & improvement

  • genome assembly

  • variant discovery

  • RNA-Seq analysis

  • experiment design

  • data visualization

  • bioinformatics IT issues

  • cloud computing mini-bootcamp

The course includes a rich collection of lectures and hands-on sessions, including guest speakers from industry and academia. All hands-on exercises will use the Galaxy platform (http://usegalaxy.org), and we will focus on Illumina and PacBio read data. Exercises will offer the chance to explore software and protocols for handling next-generation data analysis. There are no prerequisites other than familiarity with (and excitement for) general biological concepts. We will not spend time on programming concepts or command line training, but can provide pointers to those who desire experience in those fields. Prior course participants have included faculty, post docs, grad students, staff, and industry researchers.

Course seating is limited to 35 students in order to foster an effective learning environment and ensure sufficient one-on-one attention. Course tuition is $1,500 for academic or non-profit participants / $1,800 for other participants.

Course Schedule (updated August 27):

  • Monday morning (Sept. 16)

    • Welcome / Introduction by Richard Michelmore, Genome Center Director

    • Next Generation Sequencing Technologies & Fundamentals (lecture)

    • Read Quality Assessment & Improvement (lecture)

    • Introduction to Galaxy (exercise)

  • Monday afternoon

    • Read Quality Assessment & Improvement (exercise)

    • Galaxy Workflows (exercise)

    • The Galaxy Toolshed (demonstration)

  • Tuesday morning (Sept. 17)

    • Next Generation Sequence Assembly (lecture / exercise)

  • Tuesday afternoon

    • Genomic Assembly (lecture / exercise)

    • The Assemblathon Competitions & Assembly Evaluation (Keith Bradnam – Project Scientist, Korf lab)

    • Further Assembly Topics (lecture / exercise)

  • Wednesday morning (Sept. 18)

    • Alignment Topics (lecture / exercise)

    • Alignment Viewers / Browsers (exercise)

  • Wednesday afternoon

    • Variant Discovery (lecture / exercises)

  • Thursday morning & afternoon (Sept. 19)

    • RNA-Seq (lecture / exercises)

  • Friday morning (Sept. 20)

    • Ryan Kim – Manager, UC Davis DNA Technologies Core

    • Gary Schroth – Distinguished Scientist, Illumina

    • Jonas Korlach – CSO, PacBio

    • Panel Discussion, Closing Remarks

    • Discussion with speakers and students

  • Friday afternoon

    • Mini Cloud Computing Workshop

    • Informal project consulting