Computational Biology

Set of articles in the field of Computational Biology and Bioinformatics

Writing Python Wrapper for Bioinformatics Tools

The use of computational tools for data preprocessing and analysis is daily activity for any bioinformatician. Having a interdisciplinary field, a plethora of tools exist in the domain, written by developers from various fields and languages. Many times there can be multiple candidate tools exists to accomplish any given task. Often it is the decision …

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Molecular Docking in Google Colab

Molecular docking is an essential process in scientific drug discovery. By using the recent advances in generative deep learning the runtime required for such docking studies can be reduced significantly without comprimising accuracy compared to traditional methods. In this article, let us get familiarize ourselves with one open-source molecular docking codebase. The codebase named DiffDock …

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Visualizing 3D Protein Structures and Exporting Into images Using Jupyter Notebook.

The Jupyter Notebook is best suited for doing as well as documenting empirical research. It can contain text, code images, videos, interactive content, and also nicely typesetting equations. This makes anyone doing simulations or empirical research prototype their work and share it with their colleagues. In this blog post, I am going to show how …

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Bivariate Gaussian Distribution

Hacking the Bivariate Gaussian Distribution

In one of our earlier posts, we have seen how we can visually relate the parts of the one-dimensional Gaussian distribution equation. In this post, we will follow the same strategy to understand the terms that comes up with a Multivariable Gaussian distribution. We will focus on the Bivariate Gaussian distribution as distributions of higher-order …

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Normal distribution visual explanation

Gaussian Distribution Explained Visually

Gaussian distribution appears in various parts of science and engineering. Apart from a distribution often appear in nature, it has got important properties such as its relation to Central Limit Theorem (CLT). The figure above shows one-dimensional Gaussian distributions of various mean and variance values. Libraries like NumPy provide functions that can return Gaussian distribution …

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TwoStateMDP

Coding a Simple Markov Decision Process

A Markov Decision Process (MDP) is a mathematical framework used to model decision-making situations where the outcome of a decision depends on both the current state of the system and the actions taken by the decision maker. In an MDP, the decision maker is represented as an agent, and the system is represented as a …

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discount factor dynamics

Discount Factor in Reinforcement Learning

This article shows two key visual intuitions behind the usage of a discount factor in reinforcement learning with image, code, and video. Introduction Most of the advances in science and technology happened in the last 100 years. We can see mind-boggling progress in automotive, medicine, communication, energy, etc. . Among these advances, some technologies shake …

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