wiki:BIOS_BBMRI-omics_course

BBMRI omics Hands-on Course

date: March 31 & April 7, 2017
Location: SURFsara, Utrecht
BBMRI url: https://www.bbmri.nl/event/bbmri-omics-introduction-and-hands-on-application/

Program

10:00-10:15 Introduction to available omics data within BBMRI-omics.nl. Description of RNA-seq, 450k methylation, metabolomics, imputed genotypes, phenotypes and technical covariates. Data location and access. (Rick Jansen)

10.15-10.45: Introduction to the BBMRIomics R package for integrated analysis of BBMRI-omics data using R (Maarten van Iterson)

10:45-11.45: Practicum (Maarten van Iterson)

11.45-12:30: Lunch (demo: using BBMRI-Omics.nl online atlases (Jan-Bert van Klinken))

12.30-13.00: Joost Verlouw: QTL lookup of GWAS hits. Take the SNP hits from a recent GWAS, extract corresponding BIOS genotype data, run association with full Methylation, Expression and Metabolomics data sets.

13.00-14.00: Practicum (Joost Verlouw)

14.00-14.15- Tea break

14:15-14:: Introduction to the Brainshake 1H-NMR metabolomics platform (Marian Beekman)

14:45-15.30: Practicum. Analyzing Metabolomics data (Koen Dekkers)

15:30-16:00: Allele specific expression (Niek de Klein & Freerk van Dijk)

16:00-17:00: Practicum (Niek de Klein & Freerk van Dijk))

17:00 Drinks

Practicum guidelines and exercises

http://bios-vm.bbmrirp3-lumc.surf-hosted.nl/BBMRIomics_HandsOn/

Allele specific expression practicum is attached below.

Virtual machines used during the course

Thanks to the support of SURFsara, we could use run VMs on their HPC cloud for the hands-on training. Two servers will be available during the training day.

  • alpha.bbmrirp3-lumc.surf-hosted.nl
  • bravo.bbmrirp3-lumc.surf-hosted.nl

Depending on which login you got assigned, you can access the command line terminal of the VM using:

 ssh alpha<a number assigned to you>@alpha.bbmrirp3-lumc.surf-hosted.nl
 ssh bravo<a number assigned to you>@bravo.bbmrirp3-lumc.surf-hosted.nl

Depending on which team you are assigned to, you can access the Rstudio interface of the VM using:

Last modified 7 months ago Last modified on Apr 4, 2017 8:16:36 PM

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