Computing

You just committed a large file and can't push to GitHub

Oh ohh! 😱 What do you do now? The data me and my colleagues work with is typically too big for our personal computers, so we use a high performance computing environment (cluster) and mostly interact with it through the command line terminal.

Asking for help is challenging but is typically worth it

Recently I’ve been thinking on the subject of asking for help. In short, it’s hard to ask for help. It involves admitting to yourself that you can’t solve the problem alone, opening yourself up, hoping that another person will understand you and guide you in the right direction.

Login to the cluster, request a node and change to your project directory in a single command

To be able to do RNA-seq research work in large multi-sample studies you have to be able to analyze large files and thus frequently use a powerful computing environment. In my case, this means that I have to login to a computing cluster frequently.

Quickly making posters with PosterGenius

It is time to revive Fellgernon Bit from it’s deep hibernation period. A couple of very motivated Ph.D. students from my department (John, Alyssa, Amanda, Jean-Philippe, Elizabeth, etc) are organizing a blogging group.

Alfred: a must for any Mac user

At the beginning of the semester, I decided to go hunting for Mac apps that would help me be more organizing and/or enjoy my Mac even more. After all, I was using the basics –with multiple spaces– and had only customized my favorite editors.

me: Bad rm, don't delete stuff I didn't want to delete! (rm: well, I do what you tell me to do!)

When Sandy was in town at some point I started doing some of my research work, but I shouldn’t have. I basically did a silly mistake and erased files that take a long time to compute.

Bitbucket revamped

Bitbucket announced their new “look” today. The goal is to make it more team friendly but I guess that they also wanted to make it look fresh. For example, the overview page now has a quick summary:

Introducing Git while making your academic webpage

Last week I gave a presentation during our computing club on how to use git (a version control system). I used as a motivating example the first steps of creating your own academic webpage.

Version control: need to learn Git

I consider myself a fan of using version control for bioinformatics/biostatistics (or any text based, like code) project. Yet my knowledge of version control systems is quite limited. I’ve used Mercurial for some time, but I haven’t ventured much beyond the basic commands and some GUIs for merging.

Setting up your computer for bioinformatics/biostatistics and a compedium of resources

Jumping on the train set by Hilary Parker “The Setup (Part 1)" and Alyssa Frazee “my software/hardware setup”, I’m going to share my setup and hopefully add something new. They both did a great job already, so make sure you read their posts!