Spring 2024 EEOB/BCB 546 Schedule

We will update this page before every class with the slides and links to in-class materials. To view the planned schedule of course activities, view the class calendar using the button below.

Class Calendar

Accessing Data and Class Files

All of the files used for in-class activities and assignments are published online in a public GitHub repository. It is expected that you will pull any new changes to this repository at the beginning of class. This will enable you to access new data files and scripts needed for in-class activities.

The Spring 2024 repository can be found at: https://github.com/EEOB-BioData/BCB546_Spring2024.

You will also need to access the files associated with the course textbook Bioinformatics Data Skills by Vince Buffalo. This repository can be found here: https://github.com/vsbuffalo/bds-files.

In Class Activities

• In person sessions: 1:10 PM to 2:30 PM in 0030 Bessey Hall.

Current Week

April 24-26

• Apr 24: VB, Chapter 12: Bioinformatics shell scripting, writing pipelines, and parallelizing tasks [tutorial]
• Apr 26: VB, Chapter 12: Bioinformatics shell scripting, writing pipelines, and parallelizing tasks [tutorial

Previous Weeks

January 17-19

• Jan 17: Introduction to the Course [slides] [UNIX_exercise]
• Jan 19: VB, Chapter 3: Getting started with Unix [slides]

January 24-26

• Jan 24: VB, Chapter 3: Getting started with Unix [slides]; VB, Chapter 7: Advanced Unix [slides]
• Jan 26: VB, Chapter 7: Advanced Unix [slides]

January 30-February 2

• Jan 30: VB, Chapter 7: Advanced Unix [slides]
• Feb 2: VB, Chapter 7: Advanced Unix [slides]

February 7-9

• Feb 7: Chapter 7: Advanced Unix [slides]; High Performance Computing at ISU [slides]
• Feb 9: VB, Chapter 4, 5: Intro to Version Control using Git [slides]

February 14-16

• Feb 14: More on Git [slides]
• Feb 16: Intro to R [website]

February 21-23

• Feb 21: R Data Structures [website]
• Feb 23: R Data Subsetting and Transformation [website]

February 28 - March 1

• Feb 28: R Data Transformation [website]
• Mar 1: R Data Visualization [website]

March 6-8

• Mar 6: R Data Visualization [website]
• Mar 8: R Frunctions and Scripts [website]

March 13-15

• Spring Break

March 20-22

• Mar 20: Data Management Plans and LaTeX [slides]
• Mar 22: Introduction to python: [website][slides], Setting up Jupyter on Nova, [slides]

March 27-29

• Mar 27: Introduction to python (part 2): [website], [slides], Jupyter Tips and Tricks [slides]
• Mar 29: Pandas Dataframes [website], [slides], in-class [exercise 1]

April 3-5

• Apr 5: Pandas (part 2) [website], in-class [exercise 1], [exercise 2]
• Apr 7: Data Visualization with Seaborn [website], [slides], in-class [exercise 1].

April 10-13

• Apr 10: Data Visualization with Seaborn (part 2) [website], in-class exercise, plotting [DESeq2], [GFF3], and [TSV] datasets.
• Apr 13: Introduction to Biopython [website], [in-class].

April 17-19

• Apr 17: Biopython cheatsheet [slides], in-class [exercise 1]
• Apr 19: VB, Chapters 10-11: Sequencing & Alignment Data [slides]

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