Workshop Materials

Slides

The slides from the day, as a single HTML file that opens in any web browser:

Notebooks

The workshop notebook, ready to run in Colab:

Open the workshop notebook

Use File → Save a copy in Drive to get your own editable copy.

To run it on your own machine instead:

  1. Download the notebook (9.8 MB).
  2. Make a folder for the workshop and put the notebook in it.
  3. Open that folder in VS Code or Jupyter, then open the notebook.

Work from that folder throughout. The papers you download and the files the pipeline writes all land there.

Installation

Two separate packages, one for each half of the day. Both need Python 3.11 or newer.

For downloading papers (morning): tmsr-doi-downloader, from the eScience Center:

pip install tmsr-doi-downloader

For the causal map (afternoon): theoryminer:

pip install theoryminer

In a notebook or Colab, put a % in front: %pip install theoryminer.

One key to set

The downloader’s Unpaywall source needs an email address, in a .env file in your working directory:

UNPAYWALL_EMAIL=your.email@example.com

No GPU needed. In Colab, Runtime → Change runtime type → T4 GPU is faster and free.