Syllabus

Lectures and Exercises

Daily from August 15 - August 19 and August 22 - August 26. Generally, students will be expected to participate in lectures and exercises from 10 am to 5 pm. For details about the program see the description of individual lectures.

General Schedule

9:30 am - 10 amSolutions Q&ACountway 403
10 am - 12 pmLectureCountway 403
12 pm - 1 pmLunch (on your own) 
1 pm - 2 pmIntroduction to Exercises and Q&ACountway 403 (exceptions: August 16 in Countway 424 and August 18 in Countway 506 - Minot Room)
2 pm - 4 pmWork on Exercises (on your own) 
4 pm - 5 pmQ&ACountway 403 (exceptions: August 16 in Countway 424 and August 18 in Countway 506 - Minot Room)
8 pmSolutions Released 

Preparation

Please complete the steps below before the first day of the bootcamp:

  1. Apply for an Orchestra account and enter the following information into the form:
    • Research Summary: For DBMI Quantitative Methods Bootcamp exercises.
    • Storage: Default will be sufficient.
    • Compute: A couple of jobs that will run for a few of hours (<12) spread out over the two weeks of the bootcamp.
    • Software: Latest stable release of R.
  2. Complete the following DataCamp courses:
  3. Install RStudio
  4. Create a GitHub account
  5. Read required papers for Day 1

Reading

The lectures of this course will be using data and analysis examples from the publications listed below.

  • By Day 1
    • Required: An integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR and NF1. Cancer Cell 17:98 (2010). doi:10.1016/j.ccr.2009.12.020
    • Required: The somatic genomic landscape of glioblastoma. Cell 155:462. (2013) doi:10.1016/j.cell.2013.09.034
    • Optional: Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455:1061 (2008). doi:10.1038/nature07385
  • By Day 5

Grading and Teams

Students will not receive a grade for this course. However, students are strongly encouraged to post their solutions to the exercises to a (private) GitHub repository to give other students the opportunity to see alternative solutions.

Students may work on the exercises in pairs. Students are encouraged to find partners who have a similar level of previous experience.

Course Materials

Materials such as lecture slides, exercises, and solutions will be added to the hms-dbmi/qgb-2016-students GitHub repository. In order to be able to access this private repository, students need to send their GitHub username to the course directors.