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Getting Started with

Reproducible Research

Inspired by Reproducibility for Everyone (https://www.repro4everyone.org/)

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Code of Conduct

  • Carpentries Code of conduct
    • Use welcoming and inclusive language
    • Be respectful of different viewpoints and experiences
    • Gracefully accept constructive criticism
    • Focus on what is best for the community
    • Show courtesy and respect towards other community members
  • Full Code of Conduct here: https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html
  • Contact Sarah Stevens (sarah.stevens@wisc.edu) if you experience a code of conduct violation and we will help you with how to report.

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Schedule

  • Introduction
  • Referencing and Citation
  • Planning Research
  • Experimental Reproducibility
  • Sharing, Collaborating, and Publishing
  • Analysis and Computation
  • Visualization and Images
  • Breaks tentatively at
    • Morning: 10:30 - 10:45
    • Lunch: 12 - 1 pm
    • Afternoon: 2:30-2:45

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Introductions

  • Instructors
  • Introduce yourself to your table
    • Name
    • Department/Program/Company
    • Describe your research in 3 keywords. Then follow up with a couple sentences.
    • Write one thing you’d like to learn more about in this workshop.
  • Etherpad: https://pad.carpentries.org/reproducible-research-2020-01-22
    • We’ll use this throughout the day to post slides, resources, other notes

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Other Logistics

  • Gendered bathrooms between floors in the eastern stair well (Male between 11-10, Female between 10-9)
  • Accessible and gender neutral bathroom on 10th floor (about halfway down the hallway)
  • Do you need a fridge and microwave at lunchtime? Room 1017. Someone can take you now.
  • Tea and coffee will be around all day in room 11XX.
  • Snacks will be provided at the morning and afternoon breaks in room 11XX.

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Motivation for this Workshop

  • Go to b.socrative.com/login/student
  • Room name: SSTEVENS
  • Have you failed to reproduce an experiment?
  • My own
  • Someone else’s
  • Both
  • I’ve never had problems reproducing an experiment
  • I’ve never tried to reproduce an experiment

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Baker, M. 1,500 scientists lift the lid on reproducibility. Nature 533, 452–454 (2016) doi:10.1038/533452a

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https://xkcd.com/242/

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Learning Objectives

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  • Have a framework for what “Reproducibility” means
  • Know of tools for doing more reproducible research
  • Know of resources on campus that can help you with the process of making your work more reproducible

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Want to read more about reproducibility?

  • Nature special edition - https://www.nature.com/collections/prbfkwmwvz
  • Schloss PD. Identifying and overcoming threats to reproducibility, replicability, robustness, and generalizability in microbiome research. mBio. 2018 Jun 5;9(3). pii: e00525-18. doi: 10.1128/mBio.00525-18.
  • Collins FS, Tabak LA. NIH plans to enhance reproducibility. Nature. 2014 Jan;505:612-613. doi: 10.1038/505612a.
  • Casadevall A, Ellis LM, Davies EW, McFall-Ngai M, Fang FC. A Framework for Improving the Quality of Research in the Biological Sciences. MBio. 2016 Aug 30;7(4). pii: e01256-16. doi: 10.1128/mBio.01256-16.
  • Ravel J, Wommack KE. All hail reproducibility in microbiome research. Microbiome. 2014 Mar 7;2(1):8. doi: 10.1186/2049-2618-2-8.
  • Garijo D, Kinnings S, Xie L, Xie L, Zhang Y, Bourne PE, Gil Y. Quantifying reproducibility in computational biology: The case of the tuberculosis drugome. PLOS ONE. 2013 Nov;505:612-613. doi: 10.1371/journal.pone.0080278.
  • Noble WS. A quick guide to organizing computational biology projects. PLoS Comput Biol. 2009 Jul;5(7):e1000424. doi: 10.1371/journal.pcbi.1000424.