At the Norwegian Veterinary Institute, we are now starting an internal course in bioinformatics. This repo will contain information, documentation, tutorials etc for this course.
The instructors are:
- Karin Lagesen - comparative genomics and main organizer
- Arvind Sundaram - transcriptomics
- Thomas Haverkamp - metagenomics
We have created specific pages for each part of the course.
We will keep an archive of outgoing practical messages, like homework etc, on this webpage. Note, some information might be redacted for information security reasons.
An Etherpad is a collaborative document where all can write down notes, tips, hints, links etc. Please note, this document is public, and hence, you should not write anything there that you wouldn't talk about on the bus on your way to work!
You can find the etherpad for this course here
| Date | Subject | Taught by |
|---|---|---|
| 2017-11-30 (full day) | Virtualbox, File system, UNIX part I | Thomas/Karin |
| 2017-12-07 (full day) | UNIX part II, Abel, SLURM, ssh, File transfer (scp, rsync), editor (nano) | Arvind/Karin |
| 2017-12-14 (full day) | QC - FastQC, Trimmomatic and cutadapt, duplicates (samtools) | Arvind |
| 2018-01-11 | Intro to R | Thomas |
| 2018-01-18 | Jupyter as interface, Intro to Python | Karin |
| 2018-01-25 | File formats | Arvind |
| 2018-02-01 to 2018-03-29 | Case study (8 Weeks) | All |
| 2018-03-29 and onwards | Working with own data | All |
All participants will be handed a laptop with Virtualbox installed. All participants are expected to handle this laptop with care, and to ensure that nobody gets access to it. This laptop is yours for the duration. You have admin on this computer, but don't take this to mean that you can install whatever you want. Last but not least, this computer should only be used on the wireless network at the Institute, and should not be plugged in the wall.
Please note: do not keep data on this laptop that you cannot afford to lose. This laptop is not a storage device - this is a tool used for processing data, not for storing it.
The main reason you are given a separate computer to work on is because we will be using the software called Virtualbox. This is software that we are not allowed to use on computers connected to the network at the Institute.
Virtualbox is a program that enables you to have a computer running virtually inside your computer. You will "install" a specific version of linux inside virtualbox. This is what we will use to interface with the cluster that we will use for processing the data.
We will use the University of Oslo's High Performance Computing cluster for most of our work. For more about how Abel works. see here.
Please note: transfer and storage of data on abel is only allowed with prior approval by Karin.
You can find out more about how to use abel here.
To contact the instructors, please leave an issue in the github repo. Karin is also available on twitter, as @karinlag .
Veterinary Institute people should contact the instructors on the instructors email list, or contact Karin via her vetinst email.