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For further information, see the https://bioexcel.eu website.
These best practice guides have been developed by BioExcel:
- Biomolecular simulation data in RDMkit (ELIXIR Research Data Management Kit) [suggest changes]
- Biomolecular QM/MM with (GROMACS+)CP2K [suggest changes]
- QM/MM Simulation of Biomolecular Systems [suggest changes]
- GROMACS Best Practice Guide [suggest changes]
- Creating workflows with Common Workflow Language [suggest changes]
- HADDOCK best practice guide [suggest changes]
- How to choose which CWL workflow engine to deploy [suggest changes]
- Packaging BioCompute Objects using RO-Crate [suggest changes]
- 10 Simple Rules for making a software tool workflow-ready
- Best practices in constant pH MD simulations: accuracy and sampling
- Accurate Calculation of Free Energy Changes upon Amino Acid Mutation [preprint]
- Best Practices for Alchemical Free Energy Calculations
- A protocol for information-driven antibody-antigen modelling with the HADDOCK2.4 webserver
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.
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.
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
*.mdor*.rstfile corresponding to the rendered HTML file. - You may need to go into
docs/subfolder.
- Navigate to the
- 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
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.
The individual codes and tools developed by, contributed by and used by BioExcel have their own documentation spaces:
- GROMACS
- GROMACS documentation [suggest changes]
- GROMACS user guide
- GROMACS HowTo guides
- GROMACS reference manual
- GROMACS: Getting good performance from mdrun
- GROMACS: From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package
- NVIDIA: Creating Faster Molecular Dynamics Simulations with GROMACS 2020
- HADDOCK
- HADDOCK 2.2 Manual
- HADDOCK 2.4 Manual
- HADDOCK 2.4 Tutorials
- Bonvin Lab lectures/tutorials
- HADDOCK2.4 local installation tutorial
- HADDOCK2.4 basic protein-protein docking tutorial
- HADDOCK2.4 MS cross-links tutorial
- DISVIS/HADDOCK2.4 oligomer puzzle
- HADDOCK2.4 CA-CA restraints guided docking tutorial:
- HADDOCK2.4 ab-initio, multi-body symmetrical docking tutorial:
- HADDOCK2.4 ligand binding site tutorial
- HADDOCK2.4 antibody-antigen docking tutorial
- DISVIS/POWERFIT/HADDOCK2.4 Integrative modelling of the RNA polymerase III apo complex
- Structural Bioinformatics & Modelling tutorial combining homology modelling of a protein, MD simulations as a peptide with GROMACS and protein-peptide docking with HADDOCK
- PDB tools
- PMX
- CP2K
- CPMD
- BioExcel Building Blocks (BioBB)
- BioBB tutorials
- BioBB workflows (incl workflow tutorials)
- BioBB source/docs per building block
- Building additional BioExcel Building Blocks
- Tutorial: Common Workflow Language with BioExcel Building Blocks
- Common Workflow Language
- Common Workflow Language User Guide [suggest changes]
- Introduction to Workflows with Common Workflow Language (Carpentries incubator)
- Common Workflow Language User Guide: Recommended Practices
- Dockstore: CWL Best Practices
- Arvados: Best Practices for writing CWL
- CWL 1.2 specification
- Tutorial: Common Workflow Language with BioExcel Building Blocks
- Tutorial: Common Workflow Language for Bioinformatics by Melbourne Bioinformatics
- Sharing reproducible software/workflows/data (From literature)
- FAIR Computational Workflows
- Robust cross-platform workflows: how technical and scientific communities collaborate to develop, test and share best practices for data analysis.
- Streamlining data-intensive biology with workflow systems
- Ten Simple Rules for Reproducible Computational Research
- Toward standard practices for sharing computer code and programs in neuroscience.
- Software in reproducible research: advice and best practice collected from experiences at the collaborations workshop
- Ten Simple Rules for the Care and Feeding of Scientific Data
- Ten simple rules for responsible big data research
- A review of bioinformatic pipeline frameworks
- Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers
- Research Software development
- Software Sustainablity Institute's developer guides
- Four simple recommendations to encourage best practices in research software
- 10 Simple Rules for making a software tool workflow-ready
- Ten Simple Rules for Developing Usable Software in Computational Biology
- Ten simple rules for documenting scientific software
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.
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