Computing

This work was done by Leo with Erik Nelson and Ryan Miller. Thank you for your time and input! Oh ohh! My GitHub repository is huge! 😱 What do I do now?

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.

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.

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.

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.

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.

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 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:

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.

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.