Current open research practice in Computational Biology

Stephen J Eglen

Current open research practice
in Computational Biology


Stephen J Eglen                  Cambridge Computational Biology Institute
https://sje30.github.io          University of Cambridge
sje30@cam.ac.uk                  @StephenEglen

Slides: http://bit.ly/eglen_liber2016

LIBER 2016 Workshop 8: Making open the default


Acknowledgements

Danny Kingsley; Laurent Gatto (slides); Scott Chamberlain (rcrossref).

These slides are available under a creative common CC-BY license.

Making open the default

Inverse problems are hard

Score (%) grade
70-100 A
60-69 B
50-59 C
40-49 D
0-39 F

Forward problem

I scored 68, what was my grade?

Inverse problem

I got a B, what was my score?

Research sharing: the inverse problem


Ethics and value of sharing research

“Moral” reasons to share research products

Being told to do something without seeing the benefit:

  1. Funding mandates
  2. e.g. requests from “ResearchFish”
  3. “Do unto others as you would have them do unto you”

Time committment to get metadata and share.

Giving away competitive edge.

Why bother?

Moral or selfish?


Paper

Selfish reasons to share

Why not align what is good for science with what is good for scientists?

  1. Funding mandates (REF + enforcement from Wellcome Trust)
  2. Credit through data papers
  3. Leads to further collaborations (e.g. “EPAmeadev”)
  4. Fixes data bugs / errors in analysis
  5. Avoid the data loss (Vines et al 2014). e.g. students have a habit of leaving…
  6. Your future self is probably one of the main beneficiaries of sharing.

Leading by example

What to share?

How to encourage sharing

  1. We train our students in reproducible research.
  2. When reviewing papers I usually need to ask “Is data/code available?”.
  3. Working with funders and publishers to encourage sharing. preprint.

The publishing industry

Current status in the life sciences

Problems

Positives

Rise of biorxiv


Can submit directly to several journals.

cf 9000 new submissions/month to arxiv

The view from the UK

End

Markowetz maxims for reproducibility

  1. Reproducibility helps avoid disaster (Potti)
  2. Reproducibility makes it easier to write papers
  3. Reproducibility helps reviewers see it your way (Pouzat)
  4. Reproducibility enables continuity of your ideas
  5. Reproducibility helps to build your reputation (“nothing to hide”)