doc_guidelines

A set of guidelines for documenting bioinformatics tools and workflows

https://github.com/australianbiocommons/doc_guidelines

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • 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
  • Academic email domains
  • Institutional organization owner
  • JOSS paper metadata
  • Scientific vocabulary similarity
    Low similarity (15.5%) to scientific vocabulary

Keywords

infrastructure-deployment standard tool workflow
Last synced: 6 months ago · JSON representation ·

Repository

A set of guidelines for documenting bioinformatics tools and workflows

Basic Info
  • Host: GitHub
  • Owner: AustralianBioCommons
  • License: other
  • Default Branch: master
  • Homepage:
  • Size: 107 KB
Statistics
  • Stars: 6
  • Watchers: 8
  • Forks: 5
  • Open Issues: 1
  • Releases: 6
Topics
infrastructure-deployment standard tool workflow
Created almost 6 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License Citation Codemeta

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.cff and change_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:

  1. A base template for a new GitHub repository.
  2. A source of templates or ideas that you can use in your existing repositories.

Quick start guide

  1. Fork the template to reuse it for a new repository
  2. Replace the README.md with one of the files available in the documentation_templates directory, or create your own custom README here: https://readme.so/
  3. Update the recommended files, if the required information is available (LICENSE, CHANGE_LOG and CITATION.CFF)
  4. Update, or delete, the optional files (i.e. codemeta.json)
  5. Delete elements you do not require (documentation_templates directory, original README.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:

  1. Create an issue, or
  2. 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

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"
      }
    }
  ]
}

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