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Re:produce open data materials and code

Francis Gacenga
December 10, 2019

Re:produce open data materials and code

AAS presentation slides for Re:produce open data materials and code session by @fgacenga and @adamhsparks on how to make your research open data, materials and code reproducible.

Francis Gacenga

December 10, 2019
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  1. Session Plan Session Introduction reproducibility 5 minutes Research compendia brief

    introduction 5 minutes Recorded talk Prof Del Ponte 20 minutes Discussions and Q&A with speaker & panel 20 minutes Hands on activity OSF 20 minutes Review and Wrap up 10 minutes Dr Francis Gacenga, A/Prof Adam Sparks 1
  2. Reproducibility - open data, materials & code • A growing

    collection of services allow researchers to conduct and present research reproducibly • Using platforms like OSF, GitHub, Binder, Code Ocean, Colaboratory, Gigantum and Nextjournal — researchers can undertake, collate and present their code, materials and data openly. Ref: https://www.nature.com/articles/d41586-019-03366-x Dr Francis Gacenga, A/Prof Adam Sparks 2
  3. Introduction to Research Compendia A research compendium is an artefact

    that accompanies, enhances, or is a scientific publication providing: • data, • code, and • Materials (documentation) for reproducing a scientific workflow. It can be published on different platforms using the label (or tag, community, ...) research-compendium (applied on GitHub, Zenodo, OSF) or as a fallback the term "research compendium" in the description (used on GitLab). Source: https://research-compendium.science Dr Francis Gacenga, A/Prof Adam Sparks 3
  4. Thesis Papers, Articles Posters Software Tools: Journal Conference Repositories Websites

    Curated Data Sets Tools: Git – Version control Citation Managers Code <Methods, Procedures> Tools: Notebooks e.g. R, Jupyter, Binder Docker, Reprozip, Code Ocean, Next Journal, Google Colaboratory Data Collection Data Exploration then Analysis/ Modeling/ Simulation Research Activity Planning Data Collaborate & Share Results Communication Research Project Conclusion Supporting Materials Tools: R Markdown Make Google Colaboratory Research Compendium Research Data Management Plan, pre-registration report, data analysis plan Raw Data Sets Code: Methods & Procedures Processed Data Sets Versioning Research Reports Integration of packaged elements to enable others to inspect, reproduce & extend research for distribution, managing & updating Platforms: OSF, Zenodo Github, Gigantum Research Team Findable – DOI Accessible – Open, Interoperable – Std Reusable – Re:pro Dr Francis Gacenga, A/Prof Adam Sparks 4 Research Compendia
  5. Discussion • Q&A with Prof Del Ponte • Panel –

    Belinda Weaver, Adam, Francis and Emerson Dr Francis Gacenga, A/Prof Adam Sparks 7
  6. Re:produce open data, materials and code hands on creating a

    research compendium Download the files for the hands-on exercise Using the materials you have already downloaded Create a research compendium using OSF Dr Francis Gacenga, A/Prof Adam Sparks 8
  7. Review and Wrap Up Reproducible take away kit: • Session

    materials for reuse: http://bit.ly/reproS5 • DOI Link for our materials: https://osf.io/8cszw/ • License: University of Southern Queensland 2019 under a Creative Commons Attribution-NonCommercial 4.0 International License Dr Francis Gacenga, A/Prof Adam Sparks 9