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High-Performance Computing in Bioinformatics

INF5380 / INF9380 / NORBIS

This is a course organised at the University of Oslo and funded by NORBIS.

Registering for the course

Register for the course at NORBIS. If possible, please also register for the course using Studentweb at UiO.

If you are not already a UiO student or PhD guest it is now too late to earn credits for the course.

The number of slots is limited to 30. The course is full.

Changes due to the pandemic

The course will be given in person on the campus in Oslo. We strongly encourage students to be present physically. For those that are unable to be there, we will try to provide a hybrid option with streaming or recorded lectures on Zoom.

Course location

The course will be given on the campus of the University of Oslo from the 14th to the 25th of March 2022. We will use seminar room 2269 "Python" in Ole Johan Dahl's building where the Department of Informatics is located. The seminar room is located in the northern end on floor 2 of the building in Gaustadalléen 23B in Oslo.

Zoom

A Zoom meeting will be set up for streaming of the course. The lectures on 21-22 March and a few other lectures will be given remotely on Zoom.

Zoom details will be distributed by email and Mattermost.

Collaboration with Mattermost

We will use Mattermost for collaboration, questions and discussions. All teachers and students will be become members of the team. Please log in and follow the channels there. The channel Town square is the main channel, the channel Off-topic is for informal discussions, while the teachers have their own channel called bakrommet.

Course details

Please see the following pages for details about the course:

• Prerequisites
• Concepts taught in the course
• Schedule
• Exam
• Organisers and lecturers
• Wi-Fi
• Educloud Fox cluster

Required equipment

All students need to use their own laptop computer. An SSH terminal is required to access the server we will be using.

Windows users should install:

• Putty
• Gitbash Installation instructions
• Git for Windows

Useful Material

• CSC training material
• Douglas Eadline: High Performance Computing for Dummies
• Victor Eijkhout: Introduction to High-Performance Scientific Computing (Free, CC-BY)
• Git for research
• Sigma2 HPC and storage documentation
• pMap: Parallel Sequence Mapping Tool. Main page, Git repo

NREC cloud resources

NREC resources will be used in the course. Details to follow.

Other issues

Do not hesitate to contact Torbjørn Rognes if you have any questions about the course.