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. [...]
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 [...]
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 [...]
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 [...]
