JPLaverdure

About Jean-Philippe

Originally trained in molecular biology, I quickly realized my heart lied with bioinformatics ! (How can anyone be presented an HMM and not fall in love ?). While I spend most of my days writing Python code, I must admit I am starting to enjoy my occasional dip in R.
Rockin' out at the platform !

SNP Filtering with pyGeno

Looking over the contents of our growing blog (good job guys !), it occured to me that we had not yet posted an article pertaining to the fantastic (and homegrown !) bioinformatics resource that is pyGeno. It turns out I need to use pyGeno to generate data and it's also my turn to write a blog post, how convenient ! I'll focus the article on writing a SNP filter, which can be a bit surprising the first time you try [...]

By | 2016-12-12T15:22:42+00:00 December 9, 2016|Categories: Bioinformatics, Python|0 Comments

Simple multiprocessing in R (2nd edition)

The last time I spoke about this subject, I presented a really simple way to change an lapply call into its multicore sibling mclapply. Now while this is an extremely easy modification to implement in your code to gain substantial performance benefits, it kinda required you to be making use of the lapply function in the first place. So let's look at another way to introduce multiprocessing into your existing codebase with the use of the foreach and doMC packages. [...]

By | 2016-09-20T15:53:39+00:00 September 19, 2016|Categories: Performance, R|0 Comments

Simple multiprocessing in R

Continuing my effort to help you get the most out of your CPUs, I figured we could look into using some multiprocessing functionality available for your R scripts. While there are a few different options for running multi-core treatments on your data, we'll focus on something really simple to put in place. A while back, I was putting together a script to run a large series of logistic regressions (using the glm package) in an attempt to model some data. [...]

By | 2016-03-14T15:40:03+00:00 March 14, 2016|Categories: Performance, R|Tags: |0 Comments

Grep parameters every bioinformatician should know

Your shell, along with the myriad command line programs it exposes is clearly a great friend when it comes to file manipulation. And let's face it, file manipulation is a big part of a bioinformatician's daily workload. Now, since we rarely have the time to review all the options offered by the different programs I thought I'd list some really useful ones from grep. I expect everyone to know what grep is and what it does so let's just get [...]

By | 2016-02-09T14:20:48+00:00 November 27, 2015|Categories: Bioinformatics, Data Analysis, Shell scripting|Tags: , |0 Comments

Put Those CPUs to Good Use !

If you're like me, you've probably noticed that, by default, the python scripts we write only use a portion of the processing power at our disposal.. As such, you've probably said to yourself: Hey, I paid good money for a quad-core CPU ! What's happening ? While it's true that nowadays, most CPUs are multi-core, the code we write must also be tailored appropriately in order to make use of more than one at a time. So let's dive into [...]

By | 2017-04-12T11:53:19+00:00 July 12, 2015|Categories: Performance, Python|Tags: |0 Comments