This document is the syllabus for this course.
Time: 3:20PM-4:40PM, Tue & Thu, Sep 29 - Dec 6 2022
Class Location: B1-072/074 (Weintraub Building, Fred Hutch SLU campus)
TA Office Hours: 11AM-12PM Thu (Jacob), 1:00PM-2:00PM (Avi) Wed, Oct 5 - Dec 7 2022
TA Office Hours Location: Zoom (see Slack) or the first floor of the Molecular Engineering Building in the UW Main Campus (Avi) or 2nd floor of Steam Plant @ Fred Hutch
Materials for each lecture will be available in this repository prior to the class session; the link for each topic will take you to the folder containing materials for that class. Please note that materials are considered in draft form until the beginning of the class session in which they will be presented (or if otherwise indicated).
For further assistance, TAs Avi Swartz and Jacob Greene will be available to offer assistance just after the regular class session.
- A total of 8 homework assignments will be assigned on the following dates and will be due at 1pm on the dates indicated. If you need to submit a homework late, please check with the instructor at least 24 hours before the due date.
- Grading criteria and instructions for submission are available in the Canvas site for this class.
- Submit homework solutions as Markdown text files, scripts, or PDF as appropriate for each homework through Canvas.
- You are encouraged to search online for solutions and discuss the homework with your classmates. However, the answers you submit should be written in your own words. You should also cite any online source or person that helped you arrive at your solution as inline comments in your code.
- Each homework will count for 10% of your final grade. In-class participation will count for the remaining 20%, and will be assessed from the rubric presented here.
- If you have a question about homework, please post it in the Slack workspace for this course (preferred) or message an instructor directly.
| Homework | Assigned Date | Due Date | Topic |
|---|---|---|---|
| 1 | Oct 6 | Oct 13 | Reproducible science, Git and GitHub, Markdown |
| 2 | Oct 13 | Oct 20 | Unix command line |
| 3 | Oct 20 | Oct 27 | Programming in Python |
| 4 | Oct 27 | Nov 3 | Python analysis |
| 5 | Nov 3 | Nov 10 | Modeling and machine learning in Python |
| 6 | Nov 10 | Nov 17 | Data visualization and manipulation in R |
| 7 | Nov 22 | Dec 1 | Genomic data in R |
| 8 | Dec 1 | Dec 8 | Single-cell RNA-seq analysis |
This course is designed to introduce computational research methods to graduate students in biomedical science and related disciplines. We expect students will have little to no previous experience in computational methods. This course provides a survey of the most common tools in the field and you should not expect that completion of the course will make you an expert in any single programming language. Rather, you should be equipped with foundational knowledge in reproducible computational science, and can continue learning relevant tools to suit your research interests.
Course objectives: By the end of the course, students should be able to:
- Code in R, Python, and Unix/bash shell scripting using appropriate syntax and code convention
- Select appropriate tools to perform specific programming and data analysis tasks
- Apply good practices for computational research, including project organization and documentation
- Analyze common forms of data generated by molecular biology experiments including high throughput sequencing, flow cytometry, and 96-well plate readers.
- This course will require a laptop computer, on which you should install the required software.
- Additional reading material is available for your reference.
- If you are a UW student who does not possess a prior affiliation with Fred Hutch: We will request a HutchNetID for you, which will allow access to computational resources used for this class (please note that this process requires a background check).
- Information about expectations for student conduct, disability resources, academic integrity, and religious accommodations can be found on this page.
For general inquiries about this course, please contact rasi at fredhutch.org