A graduate course covering critical computational skills for working with biological data
Instructors: Matt Hufford, Dennis Lavrov, & Tracy Heath
Time/Location: Wednesday and Friday, 1:10-2:30 PM in 334 Bessey Hall (plus Monday 1-2:30 for additional lab hours)
Web View: https://eeob-biodata.github.io/BCB546X-Fall2017
Please see the installation guide for information and updates about required software.
The topics covered in this course can all be found here: Fall 2017 Schedule. Be sure to check the schedule for updates.
A copy of the course syllabus can be found at the following link: Fall 2017 Syllabus. A pdf is also available in this GitHub repository.
- Lecture 1: Introduction to Unix [slides]
- Windows users, please see the installation guide for instructions on installing a command-line tool.
- Material for this week can be found in the Week 1 folder.
- Lecture 2: Delving more deeply into UNIX [slides]
- Lecture 1: Delving even more deeply into Unix [slides]
- Lecture 2: Introduction to high-performance computing [slides]
Be sure to get a GitHub account: https://eeob-biodata.github.io/BCB546X-Fall2017/Week_03
- Lecture: UNIX data tools [slides]
- Lecture 1: Unix continued [slides]
- Introduction to R
- More R (https://eeob-biodata.github.io/R-Data-Skills/)
- Genomic Ranges [slides]
In week 8, we will start learning Python! For these lessons, you can work on your own computer. Please be sure to follow the download/install instructions for python that we require for the class: https://eeob-biodata.github.io/BCB546X-Fall2017/Week_08.
- Introduction to Python (led by Dr. Jordan Satler)
This week we will start working with data in Python. Please be sure to pull all the recent changes from the course git repository before class.
- Lesson 1: Working with Pandas DataFrames
- Lesson 2: Indexing, Slicing, and Subsetting DataFrames
- Bonus Lesson: Reading and Writing files in Python
Please pull the course repository before class since a new data file has been added to the python-bcb546 folder.
- Lesson 1:
- Finish going over Subsetting DataFrames
- Begin Visualizing Data in Python
- Lesson 2: Visualizing Data in Python
- Lesson 1: BioPython Tutorial (Iddo Friedberg)
- Lesson 2: Sequence data and alignment
- Lesson 1: Bash Scripting (guest lecture by Dr. Walker Pett)
- Lesson 2: Data Management Plans and LaTeX (slides source and slides PDF)
- Lesson 1: More BioPython [slides]
- Lesson 2: Discussion (please consider posting questions beforehand on Slack)
December 6, Wednesday Presentations
| Order | Group Name |
|---|---|
| 1 | Udderly Confused |
| 2 | The A-MAIZE-ing Trio |
| 3 | Fernando Silva Aguilar, Henrique Uliana Trentin, Edna Mageto |
December 8, Friday Presentations
| Order | Group Name |
|---|---|
| 1 | "Unofficials" |
| 2 | E. cooli |
| 3 | Crushed Like Piggy |
| 4 | Under Caffeinated and Underpaid |
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