Paper tutorials

May 2024: Paper tutorials are under migration

These paper tutorials are in the process of being migrated to this new website. It is currently expected that some links are incorrect and some images may not display properly. We are working on fixing these.


If you are viewing this on the Chaste website, the tutorials here are static, and are only likely to work with the specific version of Chaste indicated. They are unlikley to work with the development version of Chaste.

Paper Tutorials

This is the home page for what we call Paper Tutorials.

Open-source releasing code that has been used to generate results in papers increases the credibility of the paper results, and enables other researchers to more easily build upon the results. Our aim here is to extend this idea to make it very easy to reproduce results in papers generated using Chaste.

Each paper listed below links to wiki pages associated with that paper. Here, you will find a brief introduction to the paper (including instructions on how to obtain the code and supporting data files used for the paper), and links to ‘walk-throughs’ of the code used to generate the paper results. These walk-throughs are in the same style as the main Chaste tutorials. (They are also auto-generated from comments in the actual code.) For a quick example, choose G. Mirams et al. Chaste: an open source…, and then click on one of the images.

The results of each paper are then reproducible by simply downloading the code, and running with the relevant version of Chaste. See Getting Started for more documentation on using Chaste.

Since we tend to use the Chaste build infrastructure to do our science, as well as develop Chaste itself, code like these tutorials that generates results for publication is itself a ’test’ in the Chaste framework. It is thus easy to check the results obtained when re-running against the published reference results, to ensure that the quantities of interest are unchanged (to within tolerances). This is done, for instance, in the functional curation and ICCS2013 papers.

Note that this is a new feature: the framework for setting up these paper tutorials is still being finalised, and more papers will be added in time. In the future we envisage external users, who wish to release their own documented Chaste code, also being able to contribute to these pages.









Writing paper tutorials

For instructions on how to create a new paper tutorial, see Writing Paper Tutorials.