BioExcel Documentation


Collection of documentation and Best Practice Guides for BioExcel software.

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BioExcel documentation space

Collection of documentation and Best Practice Guides for BioExcel software.

For further information, see the website.

BioExcel Knowledge Centre

Best Practice Guides

These best practice guides have been developed by BioExcel:

These guides are under development:

In addition to general best practice guidance the guides reflect experience built up over time using the codes and workflow tools in specific application areas. Individual researchers may therefore need to tailor this guidance to find the best approach in light of their particular circumstances and use cases.

Contributing to guides

Most of these guides are developed openly as living documents, and we welcome contributions and suggestions for improvements.

See suggest changes links above where you can raise an Issue or submit changes as a Pull Request with a GitHub account.

If you prefer, you can instead suggest changes to the guides by posting a question in the BioExcel forum. Please include the URL to the relevant page.

Editing with GitHub

Some of the pages are edited using Github Pages, if you are new to GitHub or contributing to Open Source you may appreciate the GitHub guides like Hello World, MarkDown and How to contribute to open source.

In short:

Guides BPG1 and BPG2 are rendered using Sphinx which uses the format reStructured Text, similar to MarkDown.

To update this documentation index page, edit at

Asking BioExcel

If you have a question not answered by the guides or the code documentation, or you have suggestions for our best pratice guides, you may also contact us on the BioExcel forum.

You can also use the BioExcel forum to suggest changes to the guides.

Code documentation

The individual codes and tools developed by, contributed by and used by BioExcel have their own documentation spaces:

These publications and white-papers by BioExcel authors include aspects of best-practice guidance:

See also BioExcel publications and the individual software project pages for a complete list of publications.

BioExcel website

The website includes several sections relevant for documentation and knowledge dissemination: