Here are some links to code and protocols that we routinely use, as well as several documents on lab policy.
Code:
We believe in openly sharing our analyses and data. Here’s our GitHub repo. We release the data and analysis associated with our publications, usually as a series of Jupyter notebooks (see Publications for specific links).
PySCA, a python (v 2.7) implementation of the statistical coupling analysis: [github]
A newer version of PySCA from the Ranganathan lab, implemented in python 3: [github]
Python workshop for Scientific Computing:
Programming and data science are key elements of modern biological research. To encourage young scientists to get started early with coding, Kim collaborated with a team of UTSW graduate students to develop a Python workshop for high school students. It will be offered through the UTSW STARS summer research program for the first time in Summer 2022.
Continuous culture of bacteria:
We often use continuous culture for our evolution and deep mutational scanning experiments. Recently, we’ve been trying out the eVOLVER platform for this, alongside our own home-built models. Here is our (also evolving) lab eVOLVER wiki.
Lab Policy:
The Reynolds lab strives to provide a supportive and intellectually rigorous environment for doing science. Below are a few important documents on lab policy and culture.
Getting started in the lab: [pdf]
Lab notebooks: [pdf]
Archiving reagents: [pdf]
Authorship: [pdf]
Leaving the lab/closing out: [pdf]
Reynolds Lab 