# Walkthrough notes

## Chris

- [X] add intro slides
- [X] explain how we see microbes
- [X] update slides on Github
- [X] explain artifact = zip file
- [X] amplicon sequencing variants
- [X] make jumps to the notebooks
- [X] trees before diversity part
- [x] mention data limitations (trimming)
- [X] project challenge?
- [x] double check and adjust subsistence

## Nick

- [X] flux direction is usually inferred from free energy (pH, temp)
- [X] constant flow = can run forever
- [X] annotate flux image
- [X] more general unique solution fluxes
- [X] maybe only simulate one diet and have the other one as exercise
- [X] label none as no L2
- [X] add legend to hairball
- [X] draw strategy for medium
- [X] fix T-SNE defaults in micom
- [X] unique growth rates
- [X] most taxa
- [X] update AGORA

# Notebooks

## 16S

- [X] include representation slide
- [X] update exercise

# 20221007

- [ ] change functional slide from sequencing -> omics
- [ ] no need to apologize :wink:
- [X] *Chris:* make the control buttons responsive with the side bar
- [ ] no need to explain all reduction methods, just mention the general idea
- [X] *Chris*: fix the media and don't touch them again before the course
- [ ] use `save_results`, `load_results` in the notebooks