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MCB 517A: Tools for Computational Biology

Class Schedule

Time: 320PM-440PM, Tue & Thu, Sep 27 - Oct 30 2018

Location: B1-072, Fred Hutch

Lecture Date Instructor
Sep 27 Jesse Bloom
Oct 2 Rasi Subramaniam
Oct 4 Rasi Subramaniam
Oct 9 Rasi Subramaniam
Oct 11 Trevor Bedford
Oct 16 Phil Bradley
Oct 18 Phil Bradley
Oct 23 Jesse Bloom
Oct 25 Trevor Bedford
Oct 30 Phil Bradley


A total of 4 homeworks will be assigned at 12pm on the following dates and will be due 1 week later at 12pm.

Assignment Date Due Date
Oct 4 Oct 11
Oct 11 Oct 18
Oct 18 Oct 25
Oct 25 Nov 1

You are encouraged to search online for solutions, and discuss the homework with your classmates. You should however write the assignment answers yourself. You should also cite the online source or person that helped you arrive at your solution as inline comment in your code.

Homeworks should be submitted only as PDF files through Note that you can export both Rmarkdown documents and Jupyter notebooks to PDF. Check before submission that the PDF file looks as you expect it to be.

If you need to submit a homework late, please check with the instructor at least 24 hours before the due date.


Each homework will count for 20% of your final grade.

In-class participation will count for the remaining 20% of your final grade.


Introduction to Course and Working Environment

Date: Sep 27

Instructor: Jesse Bloom

  • Overview of course
  • Philosophy of computational biology
  • Introduction to Markdown
  • Install dependencies for R and Python if necessary
  • Run test scripts inside Jupyter and RStudio
  • Be able to ssh into rhino cluster

Reading, Transforming, and Visualizing Data using R

Date: Oct 2

Instructor: Rasi Subramaniam

  • Read and write tsv files
  • select, filter, arrange, mutate, summarize data
  • Plot point and line graphs

Grouping and Joining Data using R

Date: Oct 4

Instructor: Rasi Subramaniam

  • Introduction to group_by
  • Joining dataframes
  • What is Tidy Data?
  • Homework 1 assigned by Rasi

Working with Genomic Data using R

Date: Oct 9

Instructor: Rasi Subramaniam

  • Parsing genomic annotations
  • Working with deep sequencing data
  • Visualizing RNA-seq fold changes

Date: Oct 11

Instructor: Trevor Bedford

  • Reproducibility and collaborative science
  • File organization and naming
  • Git and GitHub
  • Homework 1 due
  • Homework 2 assigned by Trevor

Command Line

Date: Oct 16

Instructor: Phil Bradley

  • Intro to the command line
  • more commands, eg: grep, find, cat, head
  • PATH
  • Compiling, test on rhino, “there exists software that needs to be compiled”
  • Slurm and batch jobs
  • Vim (mainly for Git commit messages) and/or "emacs -nw"

Introduction to Python

Date: Oct 18

Instructor: Phil Bradley

  • Data types: integer, float, string
  • Lists
  • Variables and constants
  • For, while loops
  • Functions
  • Homework 2 due
  • Homework 3 assigned by Phil Bradley

Biological Analyses using Python

Date: Oct 23

Instructor: Jesse Bloom

  • Dictionaries
  • String analysis and regular expressions
  • File I/O
  • Biopython

Data Structures in Python

Date: Oct 25

Instructor: Trevor Bedford

  • Matplotlib
  • Numpy
  • Iterators / list comprehension
  • Classes
  • Homework 3 due
  • Homework 4 assigned by Jesse Bloom

Modeling and Machine Learning using Python

Date: Oct 25

Instructor: Phil Bradley

  • Pandas?
  • Scipy, clustering, linear modeling
  • Scikit-learn
  • Homework 4 due

Useful References


Course Materials for Tools for Computational Biology Fall 2018






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