Blog

Learning to be productive in bioinformatics

It has been five months since I have officially started working as a professional bioinformatician. Here are some of the things I've...

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...

Walter Isaacson’s technology arc I | Where does biology stand now?

Thoughts from reading the three books: the innovators, Steve Jobs and The Code Breaker The parallel between digital and biological...

Pitfalls in bioinformatics

Knowing what not to do is easier than the converse. By not doing what is wrong, one can only do right. Experience teaches us the...

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...