Introduction

Terms defined: virtual environment

• Sooner or later you're going to want to share your findings
• And learning how the web works is fun
• Use modern Python and JavaScript tools
  • Yes, you're going to have to learn some JavaScript…
  • …but it's not as bad as you've been told
• All of these materials can be freely re-used under an open license

Setup

• Install uv for managing Python packages and virtual environments and then run:
  • uv venv in the root directory of this project to create a virtual environment in ./.venv
  • source .venv/bin/activate to activate that virtual environment
  • uv pip install -r pyproject.toml to install requirements
• To regenerate the sample data, run make datasets to:
  • install the default parameters for snailz in ./params, and
  • regenerate the sample data in ./data
  • We use Make to run tasks because every other option proved to be more complicated
• Project uses McCole to generate and check HTML
  • Run make render to regenerate the HTML in ./docs from the Markdown files
  • Run make lint at any time to check the state of the project

The Data

snailz creates synthetic data for a study of mutant snails in the Pacific Northwest.

• One or more surveys are conducted at one or more sites.
• Each survey collects genomes and sizes of snails.
• A grid at each site is marked out to show the presence or absence of pollution.
• Staff perform assays of the snails' genetic material.
• Each assay plate has a design showing the material applied and readings showing the measured response.
• Plates may be invalidated after the fact if a staff member believes it is contaminated.