BioExcel documentation space

Collection of documentation and Best Practice Guides for BioExcel software.

For further information, see the https://bioexcel.eu website.

BioExcel Knowledge Centre

Best Practice Guides

These best practice guides have been developed by BioExcel:

These guides are under development:

Primer on workflow packaging and metadata standards [suggest changes]

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:

Register/log in to http://github.com/
Open corresponding “suggest changes” repository link above.
- Navigate to the *.md or *.rst file corresponding to the rendered HTML file.
- You may need to go into docs/ subfolder.
Click “🖉 Edit” to edit file within GitHub UI. GH will make a branch in a fork repository stored under your own account.
Add/change text
- Use the corresponding MarkDown or reStructured Text syntax
- If not sure, just use plain text.
Commit, briefly summarize your changes, e.g. Fixed download link
- Commit often so changes are small!
- For larger edits/reorganization, instead raise an Issue to discuss best way forward
Raise a Pull Request (PR) to suggest we incorporate changes from your branch.
- In the PR description, briefly summarize your changes.
- Respond to comments/email notifications in case we have any questions
Further unrelated changes? Make a new PR with a new branch.

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

To update this documentation index page https://docs.bioexcel.eu/, edit index.md at https://github.com/bioexcel/bioexcel.github.io

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:

Recommendations for BioExcel Training Programme (2016) https://doi.org/10.5281/zenodo.263926
Competency framework, mapping to current training & initial training plan (2016) https://doi.org/doi:10.5281/zenodo.264231
I’ll take that to go: Big data bags and minimal identifiers for exchange of large, complex datasets https://doi.org/10.1109/BigData.2016.7840618 preprint
Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis (2017) https://doi.org/10.1007/s41019-017-0050-4
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data (2017) https://doi.org/10.1371/journal.pbio.2001414
Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv (2019): https://doi.org/10.1093/gigascience/giz095
Whitepaper on Scientific Software Development (2018) https://doi.org/10.5281/zenodo.1194634
Defining distance restraints in HADDOCK (2018) https://doi.org/10.1038/s41596-018-0017-6
Enabling precision medicine via standard communication of HTS provenance, analysis, and results https://doi.org/10.1371/journal.pbio.3000099
An enhanced-sampling MD-based protocol for molecular docking (2018): https://doi.org/10.1101/434092 (see also https://doi.org/1.1021/acs.jcim.8b00730)
The role of metadata in reproducible computational research (2020): https://arxiv.org/abs/2006.08589
BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows https://doi.org/10.1038/s41597-019-0177-4

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

BioExcel website

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

Software by BioExcel
Publications by BioExcel
Webinars by BioExcel
Training by BioExcel
BioExcel Knowledge Resource Centre
ask.bioexcel.eu forum for HADDOCK, DISVIS, POWERFIT, PRODIGY, SPOTON, PDB-tools, pmx, MDWeb, BioBB, Workflows, QM/MM, etc.
Gromacs user forum