= BBMRI omics Hands-on Course =

date: March 31, 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 [https://www.surf.nl/en/services-and-products/hpc-cloud/index.html 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

==== SSH connection ====
Depending on which team you are assigned to, 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
}}}

==== Rstudio connection ====
Depending on which team you are assigned to, you can access the Rstudio interface of the VM using:
* http://alpha.bbmrirp3-lumc.surf-hosted.nl:8787

* http://bravo.bbmrirp3-lumc.surf-hosted.nl:8787