Tasks from debrief of Beirut workshop (2023-09-18):
[ ] Better explanation of Conda and what it's used for (could be incorporated as part of a longer Unix intro).
[ ] Move exercises to their own section - participants were confused that there was a lot of content and they thought they had to read it and run the commands from it (which often didn't work).
[ ] Have a start-to-finish case study, so it's easier to see it all together (almost like a recipe).
[ ] Reporting - revise this to be about publishing their genome(s), as reporting feels too official and we are not in a position to deliver that; could change the focus so that they effectively write a draft for a mini-paper.
[ ] #15
[x] Homopolish - might be incorporated in the workflow, therefore would need some slides about it.
[ ] Switch FigTree to Microreact (or as well as).
[ ] Use Gedit instead of nano.
[ ] Pathogenwatch accounts - issues connecting from within Guacamole as participants didn't want to use their personal email within it; this is an issue more generally, as people need to have an account - is there a way to get guest accounts or something like that?
[ ] Make pre-assembled FASTA files available. This might be useful generally (if participants skip some exercises), but also useful to run Pathogenwatch outside of Guacamole.
[ ] Differentiation - materials can be quite challenging to a less experienced audience; could we think of a way to have differentiated materials?
[ ] Phylogeny - place the annotation file in an easier location.
Revised schedule
3 days is too short, especially for an audience that hasn't done Unix before.
Here is a revised schedule for 5 days:
Mon
AM: welcome & setting up (make sure can login to Pathogenwatch, Slack, Guacamole, have links to materials, etc.)
PM: Unix
Tues
AM: Continue Unix + Conda + scripts
PM: Mash
Wed:
AM: Assembly
PM: QC & annotation
Thu
AM: MLST
PM: Phylogeny (more time on FigTree/Microreact)
Fri:
AM: AMR
PM: Publishing
Extra time
Could do clinic to sit down with somebody to help install on their computers
Tasks from debrief of Beirut workshop (2023-09-18):
nano.Revised schedule
3 days is too short, especially for an audience that hasn't done Unix before. Here is a revised schedule for 5 days: