Biology is Messy, Because Physicists Failed
<p>I came across an interesting blog post titled <a href="https://gptomics.com/blog/biology_is_messy.html#fn:7">Biology is Messy</a>. The main argument is that biology is not built on top of reduction...
Mathematical Side of AI and Its Applications in Biology
<p>Right now everyone is either enamored of or is completely turned off by AI. Speaking of being fed up, please check the students at University of Florida booing <a href="https://www.youtube.com/shor...
Gene Regulatory Network Reconstruction with Single-cell Data
<p>On the subject of reconstructing gene regulatory networks (GRNs) from RNAseq and scRNAseq data, I am working through a number of review papers and the techniques described therein.</p> <ol> <li>...
Scientific Questions (and Maybe Answers) for 2021-2038
<p>In an <a href="https://homolog.us/blogs/biology/2026/05/08/history-genetics-1949-today/">earlier post</a>, I divided the modern era of genetics into 18-year periods (eras). The discoveries of each ...
Organic
<p>When I hear the word organic, two thoughts immediately come up: organic search and organic chemistry. The latter comes up because it is ingrained in me that organic chemistry is one of the hardest ...
The Perceptron - classifying items into two classes based on numerical input variables
<p>I've been reading Sebastian Raschka's excellent book <a href="https://www.amazon.co.uk/Machine-Learning-PyTorch-Scikit-Learn-learning/dp/1801819319">Machine Learning with PyTorch and Scikit-Learn</...
Benchmarking R based bioinformatics speed across different computer types
<p>As a bioinformatician, or other type of data analyst, we should be using the right tool for the job. There are many types of compute we can use from laptops, desktops, pro workstations, on prem-ser...
AI-guided data visualization of gas prices in different geographical locations across the US over time
In this blog post, I will walk through how I went from a question regarding gas prices in different geographical locations across the US over time, to using AI to help me find the relevant data for my...
In Data Analysis We Trust
<p><img alt="" src="https://divingintogeneticsandgenomics.com/img/nextflow2.jpeg" /></p>...
Installing Python libraries within virtualenv
<p> Today I learnt how to install Python libraries in a virtual environment (in my case, on the Sanger compute farm), using <a href="https://virtualenv.pypa.io/en/latest/">virtualenv</a>.</p...