- Last modified: tor nov 12, 2020 03:47
- Sign: JN
Literature course in Bioinformatics for Biologists at NRM given in the fall 2020.
The course follows the text book Computing Skills for Biologists - A Toolbox, by Allesina & Wilmes (Princeton University Press, 2019).
Accompanying web page from the publisher is here: https://github.com/CSB-book/CSB.
A fork of the CSB repository is also present in this repository as a submodule. This submodule (folder) is tracking https://github.com/Naturhistoriska/CSB.git. Expect some changes between this local copy and the original CSB repository.
To clone the BIOinfo-course repository, including the CSB submodule, use this command:
git clone --recurse-submodules https://github.com/Naturhistoriska/BIOinfo-course.git
Slack-workspace for the course: https://BIOinfo-course-2020.slack.com (requires a Slack-account and a private invitation).
| Date | Time | Venue | Topic | Chapter |
|---|---|---|---|---|
| Oct 01 | 14:00--15:00 | NRM KÖL lunchroom + Zoom | Introduction | NA |
| Oct 08 | 14:00--16:00 | NRM KÖL lunchroom + Zoom | Unix | 1 |
| Oct 15 | 14:00--16:00 | NRM KÖL lunchroom + Zoom | Version control (git) | 2 |
| Oct 29 | 14:00--16:00 | NRM KÖL lunchroom + Zoom | Basic programming (Python) | 3 |
| Nov 12 | 14:00--16:00 | NRM KÖL lunchroom + Zoom | Writing good code (Python) | 4 |
| Nov 19 | 14:00--16:00 | NRM KÖL lunchroom + Zoom | Regular expressions (Python) | 5 |
| Dec 03 | 14:00--16:00 | NRM KÖL lunchroom + Zoom | Scientific computing (Python) | 6 |
| Dec 10 | 14:00--16:00 | NRM KÖL lunchroom + Zoom | Scientific typesetting (LaTeX) | 7 |
| ? | ? | ? + Zoom | Statistical computing (R) | 8 |
| ? | ? | ? + Zoom | Data wrangling and visualization (R) | 9 |
| ? | ? | ? + Zoom | Relational data bases (SQL) | 10 |
Note, all occasions (except the first: "Introduction") will be follow-up sessions where we will share problems, solutions, and experiences from participants after solving exercises in the mentioned chapters. For some dates (indicated in bold), there are two weeks in between the meetings.
Presentation material (jupyter notebooks, .ipynb) and slides (.html) are
available in the slides folder. Clone the BIOinfo-course repository
and open the files locally (in jupyter or web browser) for best experience.
The course will consist of a series of meetings (physical and/or online) where we will go through the chapters in a recent text book in bioinformatics: "Computational Skills for Biologists - A Toolbox" by Stefano Allesina and Madlen Wilmes (Princeton University Press, 2019).
Participants are expected to get a copy of the book on their own.
Students are expected to solve the exercises in the book between each occasion, where we will discuss solutions, issues, and more.
Upon completion of the course, the participant will have training and good knowledge in important bioinformatic topics such as
- Working in a Unix/Linux environment
- Use version control (git)
- The Python programming language
- Scientific typesetting (LaTeX)
- The R programming language
- Relational databases (SQLite)
The course is aiming for some students at NRM, but anyone interested can join.
No prior knowledge in bioinformatics is needed, but participants will need a computer with suitable tools installed (help with that will be provided), in order to follow the course.
We are aiming for a start during week 40 (one of the days Tue-Fri), and the ambition is to meet once a week (or every second week - partly up to the participants). The number of occasions is somewhat dependent on the pace of the students, but the book have 11 chapters...
We will meet at NRM (room number decided later), with the possibility to join on line.
Send me an e-mail (emailto:Johan.Nylander) before September 26.