Category Archives: Software

The Pitfalls

It is ironic how easy yet difficult it is to start learning computational methods or tools. I am looking back at the first ever code I wrote in python (available at the end of my master thesis). It’s not bad at all, considering the fact that I used to, literally, hate computers in the years prior to 2009. I have used “try, except”, created classes, defined functions.

8 years have passed since I wrote that code. Although it was easy to start, how much I have progressed since then? The answer is ‘quite a lot’. Have I truly become an expert? ‘Probably not!’

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Scripts Toolbox for Protein Art

Look at me, all grown up using git and creating websites with sphinx. Why I started all this? Well to finish a course project. And also I had to obtain better programming practices. If you want to read a fancier, longer answer including why I needed better programming practices here is your answer:

Coding is an activity feared by quite a few biologists yet it is a necessary skill to have at least on beginners level within many fields of biology. Computational biology is on the far end of those fields, as it requires more knowledge on programming than biology.

Why is programming more important than the biology in this field? Well to answer this question I will summarize my own experiences as a biologist in computational biology field before I made the decision to tame my computational skills.

I have used a computer for the very first time in 2004. I have met with terminal in 2009. I have tried to learn programming by myself. However, let’s face it, no purpose means no progress. So I it wasn’t until my master thesis that I wrote a functional script. I learned Python and wrote lines of codes in the worst possible way, perhaps and those lines gave me what I needed. All was well at that point.

I started my PhD, subject is structure & function of ligand-gated ion channels. The name doesn’t strike as something extraterrestrial. It is a protein and I’m a biologist. Besides the title, everything was and is extraterrestrial. I have learned that quite many of the data on articles were generated by in house scripts or programs. Even if there was a tool, the output was not in the format you desired. Porting 5000 data points to excel and manual clicking 100 times to get a simple bar graph was meant suicide and no thesis would be finished within my life time. I had to rely on my scripting knowledge increasingly.

I am a person who learns things on the fly and gets the job done in any possible way. Then finds a way to improve it if needed. Although this motto provided me with three articles and a few more about to be published, it also damaged my sustainability. Spending the same long hours for similar analysis was just ridiculous. And that’s why I needed to obtain better practices: version control and documentation especially.

Enjoy the Scripts Toolbox for Protein Art and watch my baby grow up (sounds creepy). Just enjoy the website.