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 !

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 | 2017-04-29T15:35:48+00:00 November 27, 2015|Categories: 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 | 2017-04-24T13:28:50+00:00 July 12, 2015|Categories: Performance, Python|Tags: |0 Comments

Database Content Versioning Using SQLAlchemy

One of the important functionality required of a LIMS is keeping a history of the changes applied to the data stored within the underlying database. This can be a tricky aspect to develop and/or put in place and there are certainly a number of ways one can go about implementing such a solution. Fortunately for all you SQLAlchemy fans out there, a fully implemented versioning solution is provided in the ORM's examples page. While the examples page provides a few [...]

By | 2017-05-01T10:27:33+00:00 October 5, 2014|Categories: Computer science, Database, Python|Tags: , , , |0 Comments