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This wiki is meant as a repository for bioinformatical knowledge at the CEES. It is mainly run by Lex, but others are also very welcome to contribute.

  • If you want to be able to edit the wiki, let us know and we'll add you to the list of contributors.
  • If you add a page, please list it below! Tips for adding a page.

Compute resources

Overview

We have a mix of self-owned compute hardware and disk space, rented disk space, supplemented with an allocation on the UiO supercomputer 'Abel'. 
For details, see

Getting access

Please fill out this form: https://nettskjema.uio.no/answer/64174.html

NOTE Non-UiO staff: you will need a guest researcher account. Your collaborator from UiO will need to submit application for this, see http://www.uio.no/english/for-employees/support/human-resources/payroll/hr-payrollsystem/associated-users.html

Yearly reports

We write a yearly report on the resources and their use. See the yearly reports page.

Use of the CEES hardware and Abel

User manual cod nodes

Abel use

Installing software and creating modules

Variant calling on Abel

Tips, tricks, useful links

Organising your computational work

Useful websites with Unix commands

Useful websites with Python tips and tricks

Useful websites with R tips and tricks

Usefull small commands/scripts etc in /projects/cees

Bioinformatics knowledge present at CEES

How-to's

PacBio smrtpipe command-line use

Submitting sequences to ENA

Using virtualenv on the nodes

Quickly check the insert size distribution of a new sequencing library

Error correction of Illumina reads using merTrim from the Celera Assembler package

Assembly of Illumina paired end reads using Celera Assembler

Mailing lists

  • cees-hpc: to be used for general information related to the area under /projects/cees, the able CPUs and the cod-nodes. Subscribe here.
  • cod-nodes: to be used to inform about the other cod-node users about CPUs and memory usage of the cod nodes, aka 'cod-node hugging' :-) USIT will also send emails to that list when discs on the nodes are full etc. Subscribe here.
  • cees-bioinf: to be used for general information regarding bioinformatics at CEES. Subscribe here.