bio-ontollm

Approaches to biomedical knowledge: Ontologies and Large Language Models

Lecture series.

Quarto

Let's test out the quarto ecosystem for creating slides.

In brief:

• https://quarto.org/
• Follow installation instructions
• I am using VS Code for creating slides

Running quarto on VS Code

You will need to create a virtual environment and use to install some packages needed by the quarto ecosystem

python3 -m venv venv
source venv/bin/activate
pip install --upgrade pip
pip install numpy matplotlib pandas jupyter ikernel

Add quarto libraries

quarto add leovan/quarto-pseudocode

I have had some trouble setting up the preview within VS Code, but a workaround was to start quarto in some shell

quarto preview token.qmd

This will open up a browser window, e.g., http://localhost:7783/. Copy the address, go back to VS Code, using the command pallette enter Simple Browser Show, and paste in the address. Drag this window to the right and you will have side by side windows.

If there is a hiccup, then this command to find out the process id of quarto and kill it may come in handy

lsof -i :7783
kill -9 <pid>

where pid is the process id revealed by the lsof command.

Reset

rm -rf .quarto/ rm -rf _site/