Author Archives: Wang

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

Can a microbe grow faster later by growing slower now?

This question popped up a few years ago during a conversation with my PhD advisor. I think it makes a good riddle or exercise problem, so I’m posting it here, along with a solution I came up with. My solution … Continue reading

Posted in Literature review, Quantitative principles | Leave a comment

Tasty tomatoes and biological tradeoffs

As part of my recent fascination with plant biology, I read a paper called “A chemical genetic roadmap to improved tomato flavor“, by Tieman et al. This led me down a rabbit hole of a surprisingly large literature on the … Continue reading

Posted in Literature review, Plant biology | Leave a comment

Plant breeders were engineering biology before it was cool

Recently I’ve become fascinated1 by crop breeding and plant genetics, after realizing that these are, in a sense, the oldest fields of biological engineering. Even though we’ve only been able to manipulate genetic circuits and metabolic pathways for a few decades, we’ve been … Continue reading

Posted in Commentary, Plant biology | Leave a comment

The role of storytelling in scientific writing

I wrote this privately 2 years ago, reflecting on my first publication. Later I saw that others had already been having a similar discussion (see this piece by Yarden Katz), so I thought this would be good to share here. … Continue reading

Posted in Commentary, Life and science | 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