Uppsala Multidisciplinary Center for Advanced Computational Science

Courses and workshops

Introductory Linux courses

UPPMAX application experts want to share their skills in a 4-day series of courses. We will help you move from being a Linux novice to an UPPMAX expert. If you already have the fundamentals down, you are still sure to enjoy the tips and tricks in the later parts of the course.

This course is going to be given regularly, approximately 2 times per year. Below are links to the course webpages, with dates, places, and links to registration and course material.

The next introductory course will be held on August 21-24, 2017.

The associated Awk Workshop will be held on August 25, 2017.

Please contact Marcus Holm if you have any questions. 

Other UPPMAX courses

We would like to kindly request that you express your interest for taking the course by filling this survey. (Please note that this is not a registration form for the workshop itself.)

The "Awk workshop" is given in parallel to the "UPPMAX introductory course" which is given twice per year at the begging of each semester in Uppsala. This might not be the ideal schedule and location for the "Awk workshop."

UPPMAX/SNIC will try to find the optimal solution according to the collected data from this survey. The e-mail submitted in the survey form will be used to notify you about the next scheduled workshop.

Courses at other SNIC Centers

Any user of SNIC resources is welcome to attend courses at any SNIC center. The SNIC Training webpage has a list of upcoming courses and links to more information.

SeSE, Swedish e-Science Education, also provides courses. These are usually longer and more in-depth than SNIC training provides. You can see the courses offered on the SeSE homepage.

Biologists who work with genetics may be interested in SciLifeLab's course offering.

Links to extra material

Find below a few links to resources that might be useful as preparatory or further studies before or after the courses above.

Data Management Seminar

  • UPPMAX file systems (50 min, Douglas Scofield) video link
    • Disk, file system, and file overview
    • High-performance storage, and when it isn't
    • Storage at UPPMAX: Backup, nobackup, private, glob, scratch
  • Practical knowledge (50 min, Martin Dahlö) video link
    • Moving files to and from UPPMAX
    • Moving files between projects
    • Moving files within a project
    • Compressing files
    • Web export
  • Project data management (50 min, Niclas Jareborg) video link
    • A quick guide to organising computational biology projects
    • Data management life cycle — planning, generation, analysis, publication, and archiving with Open Access principles
    • Sensitive data

Python

  • CodEcademy 
    Learn python interactively in the browser.
  • Python introduction
    A very compact overview of the basic syntax of the python language. 
    (Inspired by the Perl Introduction)
  • Learn python in a few minutes (learnXinYminutes.com) 
    A short reference of the python language.
  • Rosalind Python course 
    Rosalind is a website specialised on teaching bioinformatics, by a number of problems that the user should solve. This course is a short introduction into python.

General Bioinformatics

SNIC Science Cloud

Old Course Webpages

Awk Workshop, Winter 2017

Visualisation Workshop, Autumn 2016

The previous introductory course was held in January, 2017