A practical guide to practicing open science
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This document provides a guide to practicing open science. It discusses transparency, reproducibility, and collaboration as key principles of open science. It then provides recommendations for openly sharing data, code, and papers. For data, it recommends using structured formats like BIDS and sharing in curated repositories. For code, it recommends using version control systems like GitHub and containerization tools like Docker. For papers, it recommends practices like preregistration, publishing preprints, and openly reviewing other works. The overall message is that open science promotes collaboration and reproducible research even if adopted incrementally.
A practical guide to practicing open science
- 1. A PRACTICAL GUIDETO PRACTICING OPEN SCIENCE Chris Gorgolewski @ChrisFiloG
- 2. What is Open Science? •Transparency •Reproducibility •Reusability •Collaborations
- 3. WHO IS A PHD STUDENT?
- 4. WHO IS A POSTDOC?
- 6. Why should you care about open science •Collaborations •Grant funding requirements •Job opportunities •Community
- 7. Roadmap 1. How to deal with data 2. How to deal with code 3. How to deal with papers
- 8. Gorgolewski KJ, Poldrack RA.A Practical Guide for ImprovingTransparency and Reproducibility in Neuroimaging Research http://dx.doi.org/10.1371/journal.pbio.1002506
- 9. DATA
- 10. Consent forms •General Data Protection Regulation •25 May 2018 •Open Brain Consent •http://open-brain-consent.readthedocs.io •Now in German!
- 11. Open Brain Consent However, by using additional data linked to your name (for example brain scans obtained from your medical records) one could potentially use your imaging or other information in our database back to you. If you change your mind and withdraw your consent to participate in this study (you can call <PI name> at <phone number> to do this), we will not collect any additional data about you.We will delete your data if you withdraw before it was deposited in the database. However, any data and research results already shared with other investigators or the general public cannot be destroyed, withdrawn or recalled.
- 12. Data organization • Brain Imaging Data Structure • http://bids.neuroimaging.io
- 13. Data organization Data sharing with yourself from the future is also a form of data sharing. A very important one.
- 14. Brain Imaging Data Structure POSTER NUMBER: 1854 BIDS.NEUROIMAGING.IO
- 15. Data repositories •Curated: •OpenfMRI.org •FCP-INDI •NITRC •Uncurated: •Data Dryad •Figshare •Harvard Dataverse
- 16. Gorgolewski, Milham, and Margulies, 2013
- 17. Data sharing fears •Scooping and Errors
- 18. CODE
- 19. Where to put your code? • GitHub • For day to day updates • Zenodo • For DOI, coauthorship and long-term preservation
- 21. How to test your code • Testing • Smoke tests + continuous integration • Assertion tests https://neurohackweek.github.io/software-testing-for-scientists/
- 22. Reproducibility reproducibility = shared code + shared environment + shared data
- 23. Sharing environments • All binary dependencies • Environment variables • Libraries • etc. Docker https://neurohackweek.github.io/docker-for-scientists/
- 24. Reproducibility of neuroimaging analyses a free online platform for sharing and analysis of neuroimaging data
- 25. OpenNeuro.org - Poster #1677 25
- 26. Misconception 1: Quality of code Lack of documentation and portability should not stop you from sharing your code.
- 27. Misconception 2: User support 1. You are not obliged to provide user support for your code if you share it. 2. Direct users to GitHub Issues or NeuroStars to avoid direct messages.
- 28. PAPERS
- 29. Preregistrations in clinical trials https://doi.org/10.1371/journal.pone.0132382
- 30. Preregistrations •OSF •AsPredicted It’s up to you how specific you want to be.
- 32. Preprints • Way around non-open access journals • A way to get feedback from the community • And use it to get your paper published • Ability to share preliminary ideas
- 33. Preprints • What makes a good preprint sever? • Exposure • Comments • DOIs • Versions
- 34. Preprint misconceptions The journal will not accept a paper that already appeared as a preprint. 95% wrong http://www.sherpa.ac.uk/romeoinfo.html
- 35. Reviews • Academic Karma allows you to publish your reviews • Signed or not • Negotiating an agreement with authors when a review is solicited by the editor
- 37. FINALLY…
- 38. The world is not black and white It’s many shades of grey
- 39. The world is not black and white Not this kind of grey…
- 40. The world is not black and white You don’t need to go all in – pick one thing and start practicing it
- 41. Questions?
- 42. Demo OpenNeuro.org - Poster #1677 42