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 am | Solutions Q&A | Countway 403 |
| 10 am - 12 pm | Lecture | Countway 403 |
| 12 pm - 1 pm | Lunch (on your own) | |
| 1 pm - 2 pm | Introduction to Exercises and Q&A | Countway 403 (exceptions: August 16 in Countway 424 and August 18 in Countway 506 - Minot Room) |
| 2 pm - 4 pm | Work on Exercises (on your own) | |
| 4 pm - 5 pm | Q&A | Countway 403 (exceptions: August 16 in Countway 424 and August 18 in Countway 506 - Minot Room) |
| 8 pm | Solutions Released |
Preparation
Please complete the steps below before the first day of the bootcamp:
- 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.
- Complete the following DataCamp courses:
- Introduction to R
- Intermediate R (requires a $25 fee to complete)
- Install RStudio
- Create a GitHub account
- Share your username with course directors: peter_kharchenko@hms.harvard.edu and nils@hms.harvard.edu
- Configure your account to use SSH keys
- 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
- Required: The Molecular Taxonomy of Primary Prostate Cancer. Cell 163:1011 (2015). doi:10.1016/j.cell.2015.10.025
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.