Computing

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. Thus it can be painful if your request for help is misunderstood, met with criticism or ignored. Regardless of these obstacles, I think that the potential rewards make it worth it.

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. This is a common task for other biostatisticians (like those that do brain imagining studies) and many other people. When I am working on a project, I generally have to login to the cluster and then change the directory to the location where I have my project files.

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. The idea is to review ideas, give suggestions, learn blogging technicalities, write blog posts, review them, and post them. It’s a great idea! Plus it should us keep our blogs active. So for my first post I am going to talk about PosterGenius.

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. It turns out that Alfred is an excellent app. The free version can get you a lot of mileage and save you lots of time by typing alt + space, then entering the keyword you want to search in Google.

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. Prior to being here, I had an alias in my bash profile like this: alias rm=’rm -i’ But when I setup my bash profile here I googled a bit to find what was the best common solution to avoid deleting stuff you shouldn’t be deleting.

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:  That can be useful coupled with the simpler navigation tabs. But I think that the best of the new tools is the ability to comment at a given commit at any line change.

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. The goal was to make it interesting to both new students (who might have been more interested on the webpage part) and older students (for whom version control should be a must). The slides and all the material is publicly available through the following Bitbucket repository: https://bitbucket.

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. I don’t recall how it all went, but I remember reading that Subversion (SVN) was much better than CVS. Also, the Bioconductor project uses SVN.

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! I have some experience with all three main OS: Windows, Linux and Mac. That being said, I know some of the basic stuff for each but I surely use Google very frequently to get help.

Are you good at programming? You probably practice a lot!

What makes a great programmer? I would have said training, motivation, a good and efficient framework for continuous learning from others such as reading blogs like R-bloggers (if you are an R programmer). Well, on the Occupational Digest blog they commented a paper where they found that the best predictor is programming knowledge. This is acquired through years of practice and makes sense. After all, even if you are a gifted person for something, if you don’t practice and learn from others you won’t get anywhere.