Workshop structure

[GavinHuttley]

• @cdrobles add links to teaching resources from Ensembl in a comment
• @cdrobles what exercises you think would be suitable and roughly the amount of time
• @cdrobles what resources exist on site? (what will be the facilities, internet connection, speed, etc...)
• @cdrobles how many people and their contact emails if possible
• @stefano what is the google collab setup, is there a DSocker image being used, can we get cogent3 (etc...) installed on there too?
• @gavin identify segments from cogent3 workshop to port over
• @gavin find our original survey so that we can revise and distribute to smbe
• @gavin get draft docker image for trialling
• @gavin sketch out new content for a hacking / sprint section at the workshop end

[cdrobles]

Hi both! Okay so this is what I have so far:

1. Teaching resources:
   a. presentation: https://drive.google.com/file/d/1yo3Aapyq4dEOAiaYuAUg0zpHPp4KXGDu/view
   b. exercises: https://colab.research.google.com/drive/1A1uZ9_h28aatOjYna_O9ONSP2pMBzrCM?usp=drive_link
2. I think the presentation may take about 50 minutes to an hour depending on the amount of questions. Then, I was thinking we can have 2 hours of the Google Colab exercises for them to familiarise themselves in the format they need to make requests and how it works. Perhaps they will get to the first three or four exercises, and can take the rest home. Then we would have 2 hours for you guys to introduce Cogent and EnsemblLite, would that work?
3. I am right now asking for details on the resources on site and the list of participants and will share that when I have it!

Thanks :) Daniela

[GavinHuttley]

Two hours will work! Thanks @cdrobles

[cdrobles]

Okay! Me again hehe - I have been assured there will be internet in the room but I don't think they have more details at the moment. I have also obtained the list of the 25 people that signed up, which I attach to this comment.
Registrados a Introduction to programmatic access to EnsEMBL.xlsx

[GavinHuttley]

Awesome @cdrobles !

[GavinHuttley]

@khiron can you modify the cogent3 workshop EnsemblLite-SMBE docker container. It needs

• in the standard user account, create a repos directory
• git clone via https the EnsemblLite (main) and Cogent3 (develop) repos into directories with the same name
• install mamba, look at instructions here
• initialise mamba for the zsh environment
• deactivate base enviroment conda config --set auto_activate_base false
• create a c312 as mamba create -n c312 python=3.12
• add to the end of .zsh mamba activate c312
• then activate the c312 environment and from the root dir of Cogent3 then EnsemblLite
• flit install -s --python which python`
• need info for users on how to configure their resource allocations in terms of numbers of CPUs and RAM

[khiron]

Ported the Phylomania Workshop's container over into branch devcontainer

Working on those updates now

[GavinHuttley]

@cdrobles I've sketched out a draft outline in #3