= 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 [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 Depending on which login you got assigned, you can access the command line terminal of the VM using: {{{ ssh alpha@alpha.bbmrirp3-lumc.surf-hosted.nl ssh bravo@bravo.bbmrirp3-lumc.surf-hosted.nl }}} 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