doc_guidelines
A set of guidelines for documenting bioinformatics tools and workflows
Science Score: 57.0%
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 11 DOI reference(s) in README -
○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.5%) to scientific vocabulary
Keywords
Repository
A set of guidelines for documenting bioinformatics tools and workflows
Basic Info
Statistics
- Stars: 6
- Watchers: 8
- Forks: 5
- Open Issues: 1
- Releases: 6
Topics
Metadata Files
README.md
Bioinformatics software documentation guidelines
Description
This repository allows anyone to create simple boilerplate documentation for any bioinformatics software, using guidelines that have been co-created by Australian BioCommons and members of the community.
- This template repository contains a set of guidelines for documenting bioinformatics software (e.g. tools and workflows).
- The initial guideline version uploaded to GitHub was informed by current documentation practices and structures used in the GitHub community.
- Subsequent versions have been modified and updated with input from Australian BioCommons engagements with infrastructure partners and the bioinformatics community.
- Typical files are included, such as a
LICENSE,CITATION.cffandchange_log.md - These guidelines will be further developed as needed to meet the requirements of the Australian BioCommons community.
You can use this repository as:
- A base template for a new GitHub repository.
- A source of templates or ideas that you can use in your existing repositories.
Quick start guide
- Fork the template to reuse it for a new repository
- Replace the
README.mdwith one of the files available in thedocumentation_templatesdirectory, or create your own custom README here: https://readme.so/ - Update the recommended files, if the required information is available (
LICENSE,CHANGE_LOGandCITATION.CFF) - Update, or delete, the optional files (i.e.
codemeta.json) - Delete elements you do not require (
documentation_templatesdirectory, originalREADME.md)
See the How-to Guide for detailed instructions
Citing this repository
If you use this template repository, or any of its documentation elements, please use the following citation:
Gustafsson, J., Davis, B., de la Pierre, M., Stott, A., Beecroft, S., Downton, M., Edwards, R., Chew, T., Samaha, G., & Al Bkhetan, Z. (2023). Australian BioCommons Documentation Guidelines (Version 1.5.0) [Computer software]
Contributing
Anyone is welcome to contribute to these documentation guidelines in the following ways:
- Create an issue, or
- Create a new branch of the repository and generate a pull request (PR)
If you have contributed, please also add your name to the section below!
Acknowledgements & attributions
The documentation guidelines template repository is supported by Australian BioCommons via Bioplatforms Australia funding and the Queensland Government RICF programme. Establishment of the repositoy was also supported by the Australian Research Data Commons (https://doi.org/10.47486/PL105) as part of the BioCommons BYOD Expansion Project. Bioplatforms Australia and the Australian Research Data Commons are enabled by the National Collaborative Research Infrastructure Strategy (NCRIS).
BioCommons would also like to acknowledge the contributions of the following individuals and institutions to these documentation guidelines:
- Johan Gustafsson (Australian BioCommons, University of Melbourne) @supernord
- Brian Davis (National Computational Infrastructure) @Davisclan
- Marco de la Pierre (Pawsey Supercomputing Centre) @marcodelapierre
- Audrey Stott (Pawsey Supercomputing Centre) @audreystott
- Sarah Beecroft (Pawsey Supercomputing Centre) @SarahBeecroft
- Matthew Downton (National Computational Infrastructure) @mattdton
- Richard Edwards (University of New South Wales) @cabbagesofdoom
- Tracy Chew (University of Sydney) @tracychew
- Georgina Samaha (University of Sydney) @georgiesamaha
- Ziad Al Bkhetan (Australian BioCommons, University of Melbourne) @ziadbkh
Citations
- Druskat, S., Spaaks, J. H., Chue Hong, N., Haines, R., Baker, J., Bliven, S., Willighagen, E., Pérez-Suárez, D., & Konovalov, O. (2021). Citation File Format (Version 1.2.0) [Computer software]. https://doi.org/10.5281/zenodo.5171937
- Spaaks, J. H., Verhoeven, S., Diblen, F., Druskat, S., Soares Siqueira, A., Garcia Gonzalez, J., & Cushing, R. (2023). cffinit (Version 2.3.1) [Computer software]. https://github.com/citation-file-format/cff-initializer-javascript
- Carole Goble, Stian Soiland-Reyes, Finn Bacall, Stuart Owen, Alan Williams, Ignacio Eguinoa, Bert Droesbeke, Simone Leo, Luca Pireddu, Laura Rodríguez-Navas, José Mª Fernández, Salvador Capella-Gutierrez, Hervé Ménager, Björn Grüning, Beatriz Serrano-Solano, Philip Ewels, & Frederik Coppens. (2021). Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory. Zenodo. https://doi.org/10.5281/zenodo.4605654
- Jon Ison and others, Tools and data services registry: a community effort to document bioinformatics resources, Nucleic Acids Research, Volume 44, Issue D1, 4 January 2016, Pages D38–D47, https://doi.org/10.1093/nar/gkv1116
- Matthew B. Jones, Carl Boettiger, Abby Cabunoc Mayes, Arfon Smith, Peter Slaughter, Kyle Niemeyer, Yolanda Gil, Martin Fenner, Krzysztof Nowak, Mark Hahnel, Luke Coy, Alice Allen, Mercè Crosas, Ashley Sands, Neil Chue Hong, Patricia Cruse, Daniel S. Katz, Carole Goble. 2017. CodeMeta: an exchange schema for software metadata. Version 2.0. KNB Data Repository. doi:10.5063/schema/codemeta-2.0
- O'Connor BD, Yuen D, Chung V et al. The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows [version 1; peer review: 2 approved]. F1000Research 2017, 6:52 (https://doi.org/10.12688/f1000research.10137.1)
Owner
- Name: AustralianBioCommons
- Login: AustralianBioCommons
- Kind: organization
- Email: systems@biocommons.org.au
- Website: https://www.biocommons.org.au/
- Repositories: 17
- Profile: https://github.com/AustralianBioCommons
Documentation for the development, deployment and/or optimisation of key community-endorsed bioinformatics tools and workflows
Citation (CITATION.cff)
###########################################################################################################
### This is an example CITATION.cff file completed for the documentation guidelines template repository ###
###########################################################################################################
### You can create your own using the blank template provided at the bottom of this file"
### Simply
#### 1. Delete the existing content (from line 10 - 46)
#### 2. Remove the "#" from the blank template (lines 53 - 62) and complete each field provided: for more information please see Druskat, S., Spaaks, J. H., Chue Hong, N., Haines, R., Baker, J., Bliven, S., Willighagen, E., Pérez-Suárez, D., & Konovalov, O. (2021). Citation File Format (Version 1.2.0) [Computer software]. https://doi.org/10.5281/zenodo.5171937
cff-version: 1.5.0
message: "If you use these documentation guidelines, please cite as below."
authors:
- family-names: Gustafsson
given-names: Johan
orcid: https://orcid.org/0000-0002-2977-5032
- family-names: Davis
given-names: Brian
orcid:
- family-names: de la Pierre
given-names: Marco
orcid: https://orcid.org/0000-0002-7429-1846
- family-names: Stott
given-names: Audrey
orcid:
- family-names: Beecroft
given-names: Sarah
orcid: https://orcid.org/0000-0002-3935-2279
- family-names: Downton
given-names: Matthew
orcid:
- family-names: Edwards
given-names: Richard
orcid: https://orcid.org/0000-0002-3645-5539
- family-names: Chew
given-names: Tracy
orcid: https://orcid.org/0000-0001-9529-7705
- family-names: Samaha
given-names: Georgina
orcid: https://orcid.org/0000-0003-0419-1476
- family-names: Al Bkhetan
given-names: Ziad
orcid: https://orcid.org/0000-0002-4032-5331
title: "Australian BioCommons Documentation Guidelines"
version: 1.5.0
doi:
date-released: 2023-MM-DD
###################################
### Blank template CITATION.cff ###
###################################
#cff-version: 0.0.0
#message: "Please cite as below."
#authors:
# - family-names: [family name goes here]
# given-names: [given names go here]
# orcid: [ORCID goes here]
#title: "Title of repository goes here"
#version: 0.0.0
#doi: [DOI goes here]
#date-released: YYYY-MM-DD
CodeMeta (codemeta.json)
{
"@context": "https://doi.org/10.5063/schema/codemeta-2.0",
"@type": "SoftwareSourceCode",
"license": "https://spdx.org/licenses/Apache-2.0",
"codeRepository": "https://github.com/AustralianBioCommons/doc_guidelines",
"dateCreated": "2020-03-27",
"datePublished": "2022-05-25",
"dateModified": "2023-08-08",
"issueTracker": "https://github.com/AustralianBioCommons/doc_guidelines/issues",
"name": "Australian BioCommons documentation guidelines",
"version": "1.5",
"description": "Template repository containing a set of guidelines for documenting bioinformatics software (e.g. tools and workflows).",
"applicationCategory": "Bioinformatics",
"funder": {
"@type": "Organization",
"name": "Bioplatforms Australia, NCRIS, Queensland Government RICF programme"
},
"keywords": [
"Documentation",
"template",
"FAIR"
],
"contributor": [
{
"@type": "Person",
"@id": "https://orcid.org/0000-0002-2977-5032",
"givenName": "Johan",
"familyName": "Gustafsson",
"email": "johan@biocommons.org.au",
"affiliation": {
"@type": "Organization",
"name": "Australian BioCommons, University of Melbourne"
}
},
{
"@type": "Person",
"givenName": "Brian",
"familyName": "Davis",
"affiliation": {
"@type": "Organization",
"name": "National Computational Infrastructure (NCI)"
}
},
{
"@type": "Person",
"givenName": "Marco",
"familyName": "de la Pierre",
"affiliation": {
"@type": "Organization",
"name": "Pawsey Supercomputing Centre"
}
},
{
"@type": "Person",
"givenName": "Audrey",
"familyName": "Stott",
"affiliation": {
"@type": "Organization",
"name": "Pawsey Supercomputing Centre"
}
},
{
"@type": "Person",
"givenName": "Sarah",
"familyName": "Beecroft",
"affiliation": {
"@type": "Organization",
"name": "Pawsey Supercomputing Centre"
}
},
{
"@type": "Person",
"givenName": "Matthew",
"familyName": "Downton",
"affiliation": {
"@type": "Organization",
"name": "National Computational Infrastructure (NCI)"
}
},
{
"@type": "Person",
"givenName": "Richard ",
"familyName": "Edwards",
"affiliation": {
"@type": "Organization",
"name": "University of New South Wales"
}
},
{
"@type": "Person",
"givenName": "Tracy",
"familyName": "Chew",
"affiliation": {
"@type": "Organization",
"name": "University of Sydney"
}
},
{
"@type": "Person",
"givenName": "Georgina",
"familyName": "Samaha",
"affiliation": {
"@type": "Organization",
"name": "University of Sydney"
}
},
{
"@type": "Person",
"givenName": "Ziad",
"familyName": "Al Bkhetan",
"affiliation": {
"@type": "Organization",
"name": "Australian BioCommons, University of Melbourne"
}
}
]
}