Computational Skills for Biological Data

Iowa State University – EEOB/BCB 546X

A graduate course covering critical computational skills for working with biological data

Instructors: Matt Hufford, Dennis Lavrov, & Tracy Heath

Time/Location: Tuesday and Thursday, 1:10-2:30 PM in 203 Bessey Hall

Web View: http://eeob-biodata.github.io/BCB546X-Spring2017

Reading Material

• Bioinformatics Data Skills by Vince Buffalo

Course Schedule

The topics covered in this course can all be found here: Spring 2017 Schedule. Be sure to check the schedule for updates.

Week 1

• Introduction (link to PDF)
• Unix Basics (link to PDF)

Week 2

• Remote Machines & Intro to Git
• More Fun with Git

Week 3

• Delving more deeply into UNIX
• UNIX Data Tools

Week 4

• UNIX Data Tools (continued)

Week 5

• Introduction to R

Week 6

• Working with and Visualizing Data in R

Week 7

• More R

Week 8

• Introduction to Programming in Python

Week 9

• Working with Pandas DataFrames
• Indexing, Slicing, and Subsetting DataFrames

Week 10

• Visualizing Data in Python
• Guest Lecture by Dr. Adina Howe from the Department of Agricultural and Biosystems Engineering: Bioinformatics Workflows using Unix and Python

Week 11

• Overview of group projects
• LaTeX [slides LaTeX source or PDF]
• Working with Range Data

Week 12

• Working with Range Data continued
• Working with Sequence Data

Week 13

• HPC Part 1

Week 14

• Bioinformatics Shell Scripting

Final Group Project

The group projects will be due at the end of the semester during the last two class meetings, where each group will give a presentation on their work.

The description of the group project can be found here:

https://github.com/EEOB-BioData/BCB546X-Spring2017/tree/master/Group_Project

Presentation Schedule

April 25, Tuesday Presentations

April 27, Thursday Presentations

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