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Basic Unix/Linux and compute cluster usage

Aim

The field of bioinformatics is rooted in UNIX/Linux. The aim of this workshop is to demonstrate basic UNIX commands, and how to use LUNARC to store data and run jobs (such as sequence alignment) using the queuing system.

Topics include

  • Navigating folders and listing files
  • Making and deleting folders
  • Copying/Moving data
  • Finding files
  • Searching for expressions in files from the command line, and joining files together
  • Compressing and extracting files
  • Getting data to Lunarc using sftp
  • Connecting to Lunarc via Thinlinc
  • Using the module system to load software
  • Setting up a job and submitting it to the queue

The detailed schedule will be distributed to accepted participants prior to the start of the workshop.

Number of participants

5-10

Entry requirements

  • Participants are expected to use their own computers.
  • LUNARC account

This workshop is organised by the Research School in Stem Cell Biology in collaboration with the StemTherapy Bioinformatics Core Facility. Please be aware that the number of participants is limited. Participation in the workshop is free of charge for members of the Research School in Stem Cell Biology.

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When and where?

January 22, 2019

Group 1: 09.00 - 12.00 at BMC I1309
Group 2: 13.00 - 16.00 at BMC I1341

Workshop leaders

Shamit Soneji
StemTherapy Bioinformatics Core Facility

Email: Shamit [dot] Soneji [at] med [dot] lu [dot] se

Stefan Lang
StemTherapy Bioinformatics Core Facility

Email: Stefan [dot] Lang [at] med [dot] lu [dot] se

Application

Applications will open on November 14, 2018 and will run until December 5, 2018.

Applicants will be informed of the outcome of their application via email within one week after the application deadline.