New interactive workbooks
You can now try tskit online! The workbooks at https://tskit.dev/explore are built using JupyterLite which allows them to be run within any modern browser, with no local installation required.
Workbooks differ from the existing tutorials by being dynamic rather than static pages. Readers are encouraged to actively run the workbook code themselves — hence the term “workbooks” rather than simply “notebooks”.
A few workbooks are intended for teaching in online workshops, others provide introductions to tskit-relevant topics (see below). We also intend to add further material.
Topic introductions
Currently the following workbooks are available:
- tskit.ipynb: an interactive tour of tskit (loading files, mutations, stats & plotting)
- simulation.ipynb: a quick introduction to simulation (msprime, slim, recapitation, multiple chromosomes)
Workshop material
A pair of workbooks exists to help explain ancestral recombination graphs (ARGs) using tskit. These include inline self-assessment questions, and are intended for use in workshops, such as that pictured below.
- WhatIsAnARG_workbook1.ipynb: Graphs and local trees, mutations, genetic variation and statistical calculations
- WhatIsAnARG_workbook2.ipynb: Types of ARG, simplification, and ARG simulation
Dataset analysis
Notebooks also exist to allow students and researchers to explore existing datasets. At the moment, there is a single such notebook, demonstrating methods for inspecting and analysing the 2.48 million sample SARS-CoV-2 ARG.
- sc2ts.ipynb: Analysing the SARS-CoV-2 (sc2ts) ARG using tskit, numpy and pandas. The tszipped ARG itself is available to manipulate directly in the browser.