Category Archives: Python

Using rsync to make a local copy of RCSB PDB

Why the pause between posts? This post comes after a long pause. The pause hasn’t been because of lack of interest, but mostly because IDRACK has been keeping busy lately. Recent activities included a nearly 4-week long crash course in Bioinformatics (two 90 minute sessions per week) , delivered through Zoom, so was accessed by… Read More »

The Protein Structure Series: Post – VII

The final post in this series has been published as a screen cast on YouTube. The final code used in the video is Disclaimer: Please keep in mind that the research question was phrased in this way to make it easy to understand and develop code to answer it. In the end of the video… Read More »

The Protein Structure Series: Post – VI

In this series so far, we have looked at protein structure data and introduced a bit of python code to analyse it. The code below loads a protein structure and allows the user the extract the protein’s amino acid sequence. In this post we will try to extract more information from the sequence we have… Read More »

The Protein Structure Series: Post – V

From last time In the last post, we moved from explaining the theory of proteins, especially their 3D structures to actually handling the structures with python in the jupyter notebook. If you are new here please have a look at the preceding posts to catch up. In this post, I will assume you have looked… Read More »

Parallel programming with Python: Recalculating Pi

The previous post illustrated in a simple way the use of Python for scientific computing purposes. This article extends the previous post by introducing the concept of parallel programming. The previous example will be used, so if you haven’t run that yet, I suggest you do that now. Modifications will be made to the previous… Read More »

Python: A Monte Carlo simulation to calculate Pi

Building on the previous post, which covered a very simple example using a for loop, this post will take things up a notch. As discussed before, there are many resources available on the internet for learning Python. This blog doesn’t attempt to teach you Python. Instead it provides exposure on using the Python programming language… Read More »

Programming with Python: A simple example

Python: Python is a scripting language that is commonly used in scientific computing. Being popular amongst researchers and growing in popularity by the day, it is a very important skill set to have for young people to be successful in their careers. So after that opening note lets get down to programming. There are many… Read More »