If you landed here from an old link, please update your remotes and bookmarks. Thanks!

b2slab website

This is the b2slab website.

Contributing

Guys and girls, an important note: - Please I need each one of you to (staff/phd/visitors and all) fill out this form. You will need a picture of yourself, square format, of around 640x640px approx tp fill the form. - This is required as the new website will pull everyone of us from the linked google spreadsheet. You can see the tests if this on the deployed new site at http://b2slab.upc.edu. Some random notes about the website: - Now the website pulls the team info from the linked google spreadsheet - It also pulls the publications list from futur.upc.edu. Remember you need to add all your production to drac so it is uploaded there. - We will all need to create personal websites. - The website is coded with quarto. This means that is essentially build with markdown. You can create a quarto document within Rstudio with your personal website and add it to the ~web-and-comms channel. Please join all that channel as we will coordinate the content on there and release this one. I will upload at some point a nice template for a personal site.

Please find at teams/alexandre-perera-lluna folder a template for personal website, if you keep the r cells you will get your production automcatically placed form futur. To get the link in futur you need to:

  • search for your profile at https://futur.upc.edu

  • Filter for Article en revista indexada

  • Click “Exportar”

  • Click Gestior de referencies

  • Click OK

  • A file will download, discard the downloaded file, got to downloads in your browser and copy the address of the file, something like “https://futur.upc.edu/RIS/AlexandrePereraLluna/as/YXV0b3JpYUFydGljbGVSZXZpc3RhSW5kZXhhZGE=/?locale=en”, add this file in the R section on the qmd of the template.

  • Create your personal page and add a forder with your name. Create a commit to the github in theteam/folder, or send the zip to @alex

  • We neeed shinylive extension to show shiny apps like mutua dashboard

  • quarto add quarto-ext/shinylive

  • quarto add gadenbuie/quarto-base64

Deployment

call:

bash deploy.sh

You will need credentials to the b2sserver.

Bioinformatics lectures and labs manual

Both the lectures (slides) and the labs (Quarto book) of the Introduction to Bioinformatics course are imported into team/alexandre-perera-lluna/teaching/ (linked from Alex’s page under Teaching, lectures before labs). The sources live in separate places — never edit the imported files by hand:

  • Lectures: edited in the Drive folder Docencia/Bioinformatics/Talks (not a git repo). To update:

    bash scripts/sync-talks.sh        # re-renders the decks, then rsyncs _site + handouts here
quarto render                     # or bash deploy.sh to publish right away

    Use bash scripts/sync-talks.sh --no-render to re-sync an already rendered Drive copy, and TALKS_DIR=... if the Drive folder lives elsewhere. The lecture index page under teaching/bioinformatics-talks/index.html is regenerated by the script on every run (deck links are rewritten for the website, internal migration reports stay out). ~730 MB is imported, mostly lecture videos and handout PDFs, and it is committed to the repo.

  • Labs: edited in the separate bioinfolabs repository. To update:

    cd ../bioinfolabs && git pull
bash scripts/sync-bioinfolabs.sh      # renders the book and rsyncs the output here
quarto render                          # or bash deploy.sh to publish right away

Add --profile solutions to the labs sync script for the instructor edition.