Facilities and Equipment for the Course

Week A and B are carried out in a wet lab set up for microbiology and molecular biology. Weeks C and D are in a comuter lab with students logging in to a server hosting Jupyter Lab. Week E probably requires access to a lab for microbiology again, but it depends what the students decide to do.

Weeks A and B

Consult the week A lab manual for all details.

Weeks C and D

The BGS github repository contains jupyter notebooks and other resources for the bioinformatics.

Students each have an account on the University server running Jupyter Lab. They log in, and clone the repo to their working environment. All data files up to a certain size (Mb) are included. Raw data (Gb) is too large and has to be provided another way, or else the students run analyses on a subset of the data, and are provided with the outputs for the full data set.

Software is installed for students on the server via conda, and the repository contains an environment.yaml file specifying the install.

It is important to note that the Jupyter notebooks require a bash kernel in order to run the bash commands. This may need to be installed.

Week E

This week is student-led and they write an experimental plan well ahead of time. However, the experiments will be mostly concerning bacterial growth with and without antibiotics.