Selfish reasons to carry out reproducible research

Given 29 November 2019 at the Univerisity of Hull

Inspired by Markowetz F. Five selfish reasons to work reproducibly. Genome Biol. 2015;16: 274. doi:10.1186/s13059-015-0850-7

These Google slides are at https://bit.ly/35yDvIG
The slides created by me (almost all) can be considered CC0 public domain, use as you will. Some parts were created by others, I have put credit and copyright info in the speaker notes to the Google slides

Transcript

1. Selfish reasons to carry out reproducible research Dave Lunt dave.lunt@gmail.com @davelunt https:/ /bit.ly/35yDvIG
2. What is reproducibility?
3. first Why, then How
4. It's required Why be reproducible?
5. McNutt M. Journals unite for reproducibility. Science. 2014;346: 679. doi:10.1126/science.aaa1724
8. RCUK – Statement of Expectations for Postgraduate Training Students should receive training in experimental design and statistics appropriate to their disciplines, and in the importance of ensuring research results are robust and reproducible
11. It's the right thing to do It's science
12. Ask not what you can do for reproducibility, but what reproducibility can do for you Florian Markowetz
13. It will save you time and effort It will advance your career Selfish Reproducible Research
14. Who here has tried to reproduce a published analysis? Who is most likely to reproduce your work?
15. Do experiments work first time for you?
16. “Future You” will be most likely person to reproduce your work
17. Future You Previous You Previous You does not respond to emails
18. It will greatly help “future you” Selfish reasons to carry out reproducible research
19. How can we save time, effort? eg: make figures from scripts this is reproducible analysis
20. Your research will be faster and easier (and better)
21. The old way
24. Automated reproducible Manual Cumulative total effort Number of repeats Yes you will cross this point
25. Reproducibility makes it easier to write papers and respond to reviewers
26. Reproducible research will save you time and effort Reuse and recycle data generation and analysis
27. Errors are ubiquitous Retractions will hurt you Reproducibility helps your career
28. Reproducibility will help your career Reputation Rigour New collaborators Rapid Agile Future-proof
29. Choose a collaborator Rigorous, modern, open, with future-proof methods. Leading the way. Prepared and shared many of the methods you need already.
30. Projects are not unique. How will you build your career?
31. Required Helps “Future You” Easier & faster, agile Easier papers Helps your next project Builds your career Avoid major screw-ups Makes you a cool collaborator Selfish reasons to be reproducible
32. Pause But what about ...?
33. I’d rather do real science than tidy my data It's the way I’ve always done things, and I’ve got this far Excel is just fine My data and code are spread across many computers, I couldn’t do this I’ll sort this out at the end My field is too competitive, I can’t slow down to do this
34. I’m not a computational biologist
35. How?
36. 1. relax, most problems are solved
37. 2. think of it as training
38. 3. celebrate the quick wins
39. Quick win: Be part of a support community
40. Make 1 figure from a script Quick win
41. Butterfly_project - DATA -raw_data -fig1_data - FIGURES -fig1.pdf -fig2.pdf -table1.md - RESULTS -PCA -lin_regr - SCRIPTS -fig1.py - README.txt Informative names Structured Text description of what is where Spend 1 morning to organise your data Quick win => Provenance and persistence
42. 2. think of it as training
43. Wilkinson et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016;3: 160018. doi:10.1038/sdata.2016.18 Records, Coding, Workflows, & Research Objects
44. Make data open with a doi Findable Accessible Interoperable Reusable Quick win zenodo.org figshare.com osf.io For you (and for others) Yes, data can be private until you’re ready
45. zenodo.org Yes you can keep data private until publication
46. It's free osf.io
47. osf.io
49. File storage Integration of GDrive, Box, Dropbox, Git etc OSF cloud storage Everything in one place
50. Activity All changes recorded with version control Roll back to previous versions Comments and collaborations
51. Components are folders Structure and backup Robust sharing and privacy Can be published with doi
52. try osf.io Easy to organise project Easy to store & publish data Easy to collaborate Easy reproducibility
53. Making labwork reproducible protocols.io
54. It's free
55. Quick win METHODS SECTION Experimental procedures are briefly described here for context, and exact protocols and reagents are detailed in doi:1234567 and doi:987654
56. Summary
57. It will save you time & effort Selfish reasons to be reproducible Write once and iterate, faster, helps with ms, helps with reviewers, don’t start projects from scratch- build on prior reproducibility
58. It will advance your career Selfish reasons to be reproducible Fast, cutting edge, future-proof, you’ll look good, more collaborators, extra citations, avoid career-ending disasters, builds a group etc etc
59. Do not try to be completely reproducible! Shocking finale PTO...
60. Do not decide to be reproducible. Decide to be a bit more reproducible, celebrate the small wins. Spread the word. Take home message