Computing

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Multiprocessing with Pandas dataframe

Recently, I was handling large datasets stored in Pandas dataframes. Here are some learning points: [1] The native method df.iterrows()...

Notes on BLAST and its automation in Python

BLAST is a classic set of sequence alignment algorithms that is a keystone in biology. If you are new to BLAST, here are some...

Bionitio | Logging and errors

In the previous article, I introduced Bionitio and provided a simplified template. Here, we build upon the template by adding two new...

Bionitio | Software engineering template

The Pareto distribution, the statistical property that gave rise to the 80/20 rule, tells us that a small number of things (20%) can make...

Windows | Setting up the command-line for bioinformatics

Contents 1. What is WSL/ Ubuntu and how to install them 2. Installing bioinformatics tools with APT, Bioconda or source 3. Installing...

Docker | The end of the dependency nightmare

I used to struggle a lot to get some command-line software in the dark alley of science to work. And it didn't. For days. When something...