Category Archives: Data analysis

Installing Table of Contents extension to Jupyter notebook

Table of contents 2 is a very useful extension to Jupyter notebook that allows you to have a nested outline with links to all the Markdown headings in a Jupyter notebook. This is basically essential when you’re working with a … Continue reading

Posted in Data analysis, Not biology | Leave a comment

Installing Python 3 and Jupyter notebook on Mac OS

This is my preferred way to install Python and Jupyter notebook for doing scientific data analysis. There are many alternative ways of doing this that you can find on Google. I’m doing this on a MacBook Pro (Retina, 13-inch, Early … Continue reading

Posted in Data analysis, Not biology | Leave a comment

Tutorial: bulk segregant analysis in yeast

This is a tutorial on how to do Bulk Segregant Analysis (BSA) in yeast, a particular way of doing Quantitative Trait Locus (QTL) mapping. The general aim is to identify the mutations underlying a trait difference between individuals–in this case, different yeast strains. … Continue reading

Posted in Data analysis, Microbial physiology | 6 Comments

Calculating growth rate from microbial growth curves using MATLAB

Growth curve experiments are used to study the physiology of bacteria, yeast, or other micro-organisms. You inoculate cells in a nutrient medium, let them grow, and record the optical density of the culture over time with a spectrophotometer. Automated plate … Continue reading

Posted in Data analysis, Microbial physiology, Quantitative principles | 1 Comment