Data and Materials for the 2020 ISB Microbiome Course

Output

All output generated during the walkthrough can be found in the treasure chest. The easiest way to get all of that is to download the entire repository.

Part 1: Amplicon Sequencing Data Analysis with QIIME 2

Presentation: Notebook:

You can see the actual workshop walkthrough at https://gibbons-lab.github.io/isb_course_2020/16S. Press ? to get a list of available live options such as slide overviews and speaker mode. Note that some slides are grouped vertically, you can navigate the presentation using the directional buttons on your keyboard. A PDF version (lacks the output previews) is also available.

Part 2: Modeling microbiota-wide metabolism with MICOM

Presentation: Notebook:

You can see the actual workshop walkthrough at https://gibbons-lab.github.io/isb_course_2020/micom. Press ? to get a list of available live options such as slide overviews and speaker mode. Note that some slides are grouped vertically, you can navigate the presentation using the directional buttons on your keyboard. A PDF version (lacks the output previews) is also available.

For teachers

Use case

The course presentations are meant to be compatible with common equipment available to students, so they can be encouraged to open it on their smartphone (landscape mode required) while they run commands on the terminal.

This workshop focuses on the command line interface of QIIME 2 and basically works with the command line alone. So it should be usable whether you use a server, cloud, or local deployment of QIIME 2. Make sure to give clear instructions on how to connect to the server across different operating systems ☝️

In order to minimize the need to transfer files between a server and the local machine all output is pre-generated and the visualizations are included directly in the presentation.

Technicalities

How do the presentation slides work?

The presentation itself is a webpage hosted on GitHub. Basically, it renders dynamically from a markdown file that includes the course. Editing the markdown file is sufficient to change the content of the presentation.

See the reveal docs for more info.

Preview locally

Open a terminal in the docs folder in the repo and use:

python -m http.server

This will preview the talk at localhost:8000 in a browser. Editing the markdown and reloading the page should be enough.

PDF output

To generate a PDF of the course, open up the website in chromium or chrome and append ?print-pdf to the address. For instance, if you ran it locally as described above, open localhost:8000?print-pdf in the browser. Then, choose 'print to PDF' (choose margins: none).