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Towards open and reproducible neuroscience in the age of big data

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Towards open and reproducible neuroscience in the age of big data

  1. 1. Towards open and reproducible neuroscience in the age of big data Chris Gorgolewski @ChrisFiloG http://bit.ly/2ifdaeX
  2. 2. Who discovered the structure of the DNA?
  3. 3. Rosalind Franklin and photograph 51
  4. 4. Hubble telescope legacy https://www.scientificamerican.com/article/how- old-observations-are-building-hubbles-legacy/
  5. 5. ImageNet https://qz.com/1034972/the-data-that- changed-the-direction-of-ai-research-and- possibly-the-world/
  6. 6. Revisiting the Unreasonable Effectiveness of Data https://arxiv.org/abs/1707.02968
  7. 7. Maximizing the impact Getting more data out there
  8. 8. Removing barriers
  9. 9. Neuroimaging data sharing hierarchy Poldrack and Gorgolewski, 2014
  10. 10. NeuroVault stats • 35,000 maps • 1440 collections • 61% public • 21% linked • Representing 86 different journals • 296 mentions on Google Scholar
  11. 11. Ultimate consent form • Inform participants about your intention to share data • Explain the benefits • Discuss the risks open-brain-consent.readthedocs.org
  12. 12. Incentive I - policies
  13. 13. Journal policies – case of NPG Checklist with compulsory data availability declaration
  14. 14. “Badges are stupid, but they work.” – Brian Nosek
  15. 15. Journal policies – case of PloS “All data and related metadata underlying the findings reported in a submitted manuscript should be deposited in an appropriate public repository, unless already provided as part of the submitted article”
  16. 16. Incentive II - credit
  17. 17. Gorgolewski, Milham, and Margulies,
  18. 18. • Neuroinformatics (Springer) • GigaScience (BGI, BioMed Central) • Scientific Data (Nature Publising Group) • F1000Research (Faculty of 1000) • Data in Brief (Elsevier) • Journal of Open Psychology Data (Ubiquity press) • Frontiers Where to publish data papers?
  19. 19. Incentive III - analysis
  20. 20. NeuroVault benefits - decoding
  21. 21. NeuroVault benefits – similarity search
  22. 22. NeuroVault benefits – similarity search
  23. 23. NeuroVault benefits – Gene decoding Gorgolewski KJ, Fox AS, Chang L et al. Tight fitting genes: finding relations between statistical maps and gene expression patterns. F1000Posters 2014,5:1607 (poster)
  24. 24. NeuroVault benefits - Gene decoding
  25. 25. a free online platform for sharing and analysis of neuroimaging data
  26. 26. OpenNeuro.org - Poster #1677 28
  27. 27. Demo OpenNeuro.org - Poster #1677 29
  28. 28. OpenNeuro - available Pipelines • FMRIPREP • MRIQC • C-PAC • FreeSurfer • ndmg • SPM • BARACUS • MAGeTBrain Coming soon: • QAP • OPPNI • automatic analysis • TRACULA • BROCCOLI 30
  29. 29. MRIQC – Quality control for structural and functional images MRIQC.ORG
  30. 30. OpenNeuro is free to use by anyone under the agreement that the data will be made publicly available after 18 months.
  31. 31. Reproducibility Data snapshots + software containers == reproducibility
  32. 32. Maximizing the impact II Making data easier to use
  33. 33. Brain Imaging Data Structure bids.neuroimaging.io
  34. 34. OpenNeuro - Preprocessed data
  35. 35. Science in the age of Open Data
  36. 36. Faster Going from hypothesis to answer in a couple of weeks
  37. 37. Cheaper ~$3 mln cost of reacquiring data for each of the reuses of OpenfMRI datasets (2017)
  38. 38. Higher quality Wicherts JM, Bakker M, Molenaar D (2011) Willingness to Share Research Data Is Related to the Strength of the Evidence and the Quality of Reporting of Statistical Results. PLoS ONE 6(11): e26828. doi: 10.1371/journal.pone.0026828
  39. 39. More inclusive and competitive Same datasets are available to all researchers.
  40. 40. Conclusion 1. we need to get more data in the hands of more researchers 2. building tools and platforms is crucial to achieve this goal
  41. 41. Poldracklab Know of any neuroinformatics faculty jobs? Get in touch! (asking for a friend ;)

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