MCB 536: Tools for Computational Biology

This document is the syllabus for this course.

• MCB 536: Tools for Computational Biology
  • Class schedule
  • Homework and grading
  • Course description
  • Resources and required materials
  • Instructors
  • Teaching Assistants

Class schedule

Time: 3:30PM-4:50PM, Tue & Thu, Sep 28 - Dec 5 2023

Class Location: B1-072/074 (Weintraub Building, Fred Hutch SLU campus)

TA Office Hours and Location:

• Justin: 3:00PM-4:00PM Mon, Arnold Building M1-A403 and Zoom
• Lucas: 3:00PM-4:00PM Wed, Thomas Building Double Helix Cafe and Zoom

Lecture	Date	Instructor	Topic
1	Sep 26	Rasi Subramaniam	Introduction to Computational Biology and course
2	Oct 1	TA-led	Software installation and troubleshooting
3	Oct 3	Rasi Subramaniam	VScode, Git, and project organization
4	Oct 8	Melody Campbell	Introduction to the command line
5	Oct 10	Melody Campbell	Intro to the command line (continued)
6	Oct 15	Phil Bradley	Introduction to Python
7	Oct 17	Phil Bradley	Intro to Python (continued)
8	Oct 22	Maggie Russell	Data structures and biological analyses using Python
9	Oct 24	Maggie Russell	Data structures/biological analyses in Python (continued)
10	Oct 29	Phil Bradley	Modeling and machine learning in Python
11	Oct 31	Phil Bradley	Modeling/machine learning in Python (continued)
12	Nov 5	Matthew Chan	Data analysis using R/tidyverse
13	Nov 7	Matthew Chan	Data analysis using R/tidyverse (continued)
14	Nov 12	Rasi Subramaniam	Biological sequences and annotations in Bioconductor
15	Nov 14	Rasi Subramaniam	Introduction to sequencing data
16	Nov 19	Rasi Subramaniam	Genomic data in R
17	Nov 21	Maggie Russell	Immune repertoire sequencing and analysis
18	Nov 26	Manu Setty	Single-cell RNA-seq analysis
19	Dec 3	Manu Setty	Single-cell RNA-seq analysis (continued)

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 TBD will be available to offer assistance just after the regular class session.

Homework and grading

• 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.

Here are the updated homework dates for 2024, with each date moved two days earlier:

Homework	Assigned Date	Due Date	Topic
1	Oct 3	Oct 10	Reproducible science, Git and GitHub, Markdown
2	Oct 10	Oct 17	Unix command line
3	Oct 17	Oct 24	Programming in Python
4	Oct 24	Oct 31	Python analysis
5	Oct 31	Nov 7	Modeling and machine learning in Python
6	Nov 7	Nov 14	Data visualization and manipulation in R
7	Nov 19	Nov 26	Genomic data in R
8	Nov 26	Dec 3	Single-cell RNA-seq analysis

Course description

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.

Resources and required materials

• 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.

Instructors

For general inquiries about this course or add codes, please contact GraduateEducation@FredHutch.org

• Phil Bradley
• Melody Campbell
• Matthew Chan
• Maggie Russell
• Manu Setty
• Arvind Rasi Subramaniam

Teaching Assistants

• Justin Hui
• Lucas Kampmann