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richelbilderbeek committed Jan 8, 2025
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3 changes: 2 additions & 1 deletion docs/software/vscode_on_rackham.md
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## Procedure to start VSCode

Below is a step-by-step procedure to start VSCode.
This procedure is also demonstrated in [this YouTube video](https://youtu.be/RG2FWA8yoUs).
This procedure is also demonstrated in [this YouTube video]([https://youtu.be/RG2FWA8yoUs](https://youtu.be/MkrKi5oU_po)).
An older version of this procedure is demonstrated in [this YouTube video](https://youtu.be/RG2FWA8yoUs).

### 1. Install VSCode on your local computer

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30 changes: 30 additions & 0 deletions docs/workshops_courses/bianca_intro.md
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# Introduction to Bianca: Handling Sensitive Research Data

## Overview and schedule

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Are you just beginning to work with sensitive data in your research? If yes, welcome to a 1-day introduction to handling sensitive data on the UPPMAX cluster, Bianca. We will tell you about NAISS-SENS, how to login to Bianca, transfer files via wharf, basics of the SLURM workload manager and the module system.

This is a workshop is intended for beginner users of Bianca.

You do not need to be a member of a NAISS-SENS project in order to join the workshop. A SUPR course project will be available to all participants. The workshop will consist of both lectures and exercise sessions.

**Prerequisites**: none.

**When:** Wednesday, March 19, 2024.
**Time:** 09:00 - 12:00, and 13:00 - 16:00.
**Where:** online via Zoom. Connection details will be sent to registered participants.

**Login help session:** TBD.

Registration form (soon open)

- Introduction
- Intro to NAISS-Sens
- Login: Thinlinc
- Command line intro specific to Bianca
- Module system
- Intro to transfering files to and from Bianca
- Compute nodes and slurm
- Summary
- Q/A

<https://uppmax.github.io/bianca_workshops/intro/>
10 changes: 10 additions & 0 deletions docs/workshops_courses/julia_R_matlab.md
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# Introduction to running Julia, R, and Matlab in HPC

Learn how to run Julia, R, and Matlab at Swedish HPC centres. We will show you how to find and load the needed modules, how to write a batch script, as well as how to install and use your own packages, and more.
The course will consist of lectures interspersed with hands-on sessions where you get to try out what you have just learned.

We will mainly use Tetralith at NSC for the examples for the course, but there is little difference in how you use the various HPC centres in Sweden and you should have no problems applying the knowledge to the other systems.

This course will consist of three days (9:00-16:00), one for each language. It is a cooperation between HPC2N, LUNARC, and UPPMAX.

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Dates: 24-26 March 2025.
4 changes: 4 additions & 0 deletions docs/workshops_courses/naiss_connect_transfer.md
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# Connecting to HPC systems & File transfer course

<https://github.com/UPPMAX/naiss_file_transfer_course>

16 changes: 14 additions & 2 deletions docs/workshops_courses/workshops_courses.md
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# Workshops and courses

## UPPMAX
## UPPMAX Local

- Intro to UPPMAX day 1
- [MkDocs style](https://uppmax.github.io/uppmax_intro_day_1/)
- [Sphinx style](https://uppmax.github.io/uppmax_intro/)
- [Intro to Python](https://uppmax.github.io/uppmax_intro_python/)

- [Introduction to Bianca](https://uppmax.github.io/bianca_workshops)


## NAISS centre

## NAISS centre agnostic

### Programming

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#### Python

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- [Intro to Python](https://uppmax.github.io/uppmax_intro_python/)

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- [HPC-Python](https://uppmax.github.io/HPC-python/index.html)

#### Other

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- [Introduction to running R, Python, and Julia in HPC](https://uppmax.github.io/R-python-julia-matlab-HPC/)

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- [Programming formalisms](https://uppmax.github.io/programming_formalisms_intro/index.html)
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2 changes: 1 addition & 1 deletion mkdocs.yml
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- Simons Genome Diversity Project datasets: databases/simons_genome.md
- Other bioinformatics-oriented local data resources: databases/other_local.md

# - Workshops and courses: workshops_courses/workshops_courses.md
- Support: support.md
- Workshops and courses: workshops_courses/workshops_courses.md
- Back to UPPMAX main page: https://www.uu.se/en/centre/uppmax

theme:
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