Resources and Notes

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]

 NOTES ON 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]