Nvidia GPUs Nvidia has unfortunately come to own the HPC (High Performance Computing) market, mainly through the early lead they gained with CUDA and its relative ease of use over alternatives like the more open and less proprietary OpenCL and ATI’s perhaps too late and too little GPU Open. They are certainly trying, but they just don’t seem to have enough resources behind these efforts to keep up with the latest and the install process is both not easy for the average layman (requiring a fairly new kernel) and needs pretty recent GPUs.

Screen, a Bioinformaticians Best Friend Screen is very likely the best way to keep things running in the terminal servers that you connect to. While dropping things into the background and booting them off with nohup so that they ignore the Sig Hup signal is an option, it isn’t as clean as screen and it isn’t so easy to just pick up where you left off, for instance, if you had something open in a text editor.

Installing R Properly on Ubuntu Introduction There are a lot of ‘wrong’ ways to install R. Usually the result is a system on which R does not update (e.g. installed from source), does not update as fast as upstream (e.g. installed from package manager in Debian or Ubuntu), or requires additional tools (e.g. Bioconda). These aren’t necessarily wrong, and you may need to do these at times (e.g. if you write R packages that are on CRAN, then you may need to test on a dev version, which may need to be built from source), but there is a way that is better in most cases.

Using the GWAS Catalog Finding Bipolar Related SNPs Today we will be using the GWAS Catalog to identify SNPs (Single Nucleotide Polymorphisms) that are associated with Bipolar Disorder. Sure, there is an interactive search on the page, but let’s do this locally. Navigate to the downloadable files by first clicking the ‘Download’ link on the main page, and then ‘Files’ link, you should be here: https://www.ebi.ac.uk/gwas/docs/file-downloads The main file to get is All associations v1.