Scott Edmunds, ReCon 2015: Beyond Dead Trees, Publishing Digital Research Objects. 19th June 2015

1. 0000-0001-6444-1436
@SCEdmunds
scott@gigasciencejournal.com
Scott Edmunds

2. Need to move beyond 350 year old incentive systems
Buckheit & Donoho: Scholarly articles are
merely advertisement of scholarship. The
actual scholarly artifacts, i.e. the data and
computational methods, which support
the scholarship, remain largely
inaccessible.

3. JIFBAIT Network
more
GWAS
GWAS
JIFBAIT NEWS
Arsenic Life forms, will
they take over the planet?
By Melba Ketchum, PhD
Which Overhyped, Unreproducible
Experiment Are You?
Want rapid citations for 2 years only? Carry out this quiz.
You got: STAP Cells
Of course dipping cells in
coffee will make them
pluripotent. Even if the
research gets discredited,
it’ll still get 100’s of
citations in two years.

4. The end result….
Attempts to “game the peer-review system on an industrial
scale”
1. dx.doi.org/10.1087/20110203
2. http://www.scientificamerican.com/article/for-sale-your-name-here-in-a-prestigious-science-journal/
3. http://www.scmp.com/comment/insight-opinion/article/1758662/china-must-restructure-its-academic-
incentives-curb-research
Companies offering authorship of papers made to order by
“paper mills”. Meta-analyses, network analysis & more.
Guaranteed publication in JIF journal, often using fake referees,
ID theft, etc.

5. Consequences: increasing number of retractions
>15X increase in last decade
At current % > by 2045 as many
papers published as retracted
1. Science publishing: The trouble with retractions http://www.nature.com/news/2011/111005/full/478026a.html
2. Bjorn Brembs: Open Access and the looming crisis in science https://theconversation.com/open-access-and-the-looming-crisis-in-science-14950

6. STAP paper demonstrates problems:
Nature Editorial, 2nd July 2014:
“We have concluded that we and the referees could
not have detected the problems that fatally
undermined the papers. The referees’ rigorous
reports quite rightly took on trust what was
presented in the papers.”
http://www.nature.com/news/stap-retracted-1.15488

7. STAP paper demonstrates problems:
…to publish protocols BEFORE analysis
…better access to supporting data
…more transparent & accountable review
…to publish replication studies
Need:

8. • Review
• Data
• Software
• Models
• Pipelines
• Re-use…
= Credit
}
Credit where credit is overdue:
“One option would be to provide researchers who release data to public
repositories with a means of accreditation.”
“An ability to search the literature for all online papers that used a particular data
set would enable appropriate attribution for those who share. “
Nature Biotechnology 27, 579 (2009)
New incentives/credit

9. GigaSolution: deconstructing the paper
www.gigadb.org
www.gigasciencejournal.com
Utilizes big-data infrastructure and expertise from:
Combines and integrates (with DOIs):
Open-access journal
Data Publishing Platform
Data Analysis Platform
Open Review Platform

10. Things we need to reward

11. 1. Reward Open Data

12. Data Publishing: nothing new…
Data & Metadata Collection/Experiments
Analysis/Hypothesis/Analysis
Conclusions
+ Area of Interest/Question
1839
1859
20 Yrs.

13. Data Publishing: Can be Life or Death
Climate change, global hunger, pollution, cancer,
disease outbreaks…
http://www.nature.com/news/data-sharing-make-outbreak-research-open-access-1.16966

14. To maximize its utility to the research community and aid those fighting
the current epidemic, genomic data is released here into the public domain
under a CC0 license. Until the publication of research papers on the
assembly and whole-genome analysis of this isolate we would ask you to
cite this dataset as:
Li, D; Xi, F; Zhao, M; Liang, Y; Chen, W; Cao, S; Xu, R; Wang, G; Wang,
J; Zhang, Z; Li, Y; Cui, Y; Chang, C; Cui, C; Luo, Y; Qin, J; Li, S; Li, J;
Peng, Y; Pu, F; Sun, Y; Chen,Y; Zong, Y; Ma, X; Yang, X; Cen, Z; Zhao, X;
Chen, F; Yin, X; Song,Y ; Rohde, H; Li, Y; Wang, J; Wang, J and the
Escherichia coli O104:H4 TY-2482 isolate genome sequencing consortium
(2011)
Genomic data from Escherichia coli O104:H4 isolate TY-2482. BGI
Shenzhen. doi:10.5524/100001
http://dx.doi.org/10.5524/100001
Our first DOI:
To the extent possible under law, BGI Shenzhen has waived all copyright and related or neighboring rights to
Genomic Data from the 2011 E. coli outbreak. This work is published from: China.

18. Downstream consequences:
“Last summer, biologist Andrew Kasarskis was eager to help decipher the genetic origin of the
Escherichia coli strain that infected roughly 4,000 people in Germany between May and July. But he knew
it that might take days for the lawyers at his company — Pacific Biosciences — to parse the agreements
governing how his team could use data collected on the strain. Luckily, one team had released its data
under a Creative Commons licence that allowed free use of the data, allowing Kasarskis and his
colleagues to join the international research effort and publish their work without wasting time on
legal wrangling.”
1. Citations (~300) 2. Therapeutics (primers, antimicrobials) 3. Platform Comparisons
4. Example for faster & more open science

19. 1.3 The power of intelligently open data
The benefits of intelligently open data were powerfully
illustrated by events following an outbreak of a severe gastro-
intestinal infection in Hamburg in Germany in May 2011. This
spread through several European countries and the US,
affecting about 4000 people and resulting in over 50 deaths. All
tested positive for an unusual and little-known Shiga-toxin–
producing E. coli bacterium. The strain was initially analysed by
scientists at BGI-Shenzhen in China, working together with
those in Hamburg, and three days later a draft genome was
released under an open data licence. This generated interest
from bioinformaticians on four continents. 24 hours after the
release of the genome it had been assembled. Within a week
two dozen reports had been filed on an open-source site
dedicated to the analysis of the strain. These analyses
provided crucial information about the strain’s virulence and
resistance genes – how it spreads and which antibiotics are
effective against it. They produced results in time to help
contain the outbreak. By July 2011, scientists published papers
based on this work. By opening up their early sequencing
results to international collaboration, researchers in Hamburg
produced results that were quickly tested by a wide range of
experts, used to produce new knowledge and ultimately to
control a public health emergency.

20. 1. http://www.gigasciencejournal.com/content/3/1/22
2. http://minotour.nottingham.ac.uk/
3. https://github.com/lexnederbragt/INF-BIOx121_fall2014_de_novo_assembly
1st Nanopore MinION E. Coli
genome released via GigaDB
10th September 2014 (>125GB)
Data Note peer reviewed &
published 20th October1
Immediately used for teaching
materials2 & real-time tools3

21. Real time sequencing era needs real time publication!
• First nanopore clinical
amplicon sequencing paper (&
data) published March 2015
• Can determine virus/bacteria
strains in hours
• Already in use tackling Ebola
in West Africa
• “Living internet of things”
http://www.gigasciencejournal.com/content/4/1/12

22. IRRI GALAXY
Rice 3K project: 3,000 rice genomes, 13.4TB public data
Feed The World With (Big) Data

23. OMERO: providing access
to imaging data
Already used by JCB.
View, filter, measure raw
images with direct links
from journal article.
See all image data, not just
cherry picked examples.
Download and reprocess.
Need for better handling of imaging data

24. The alternative...
...look but don't touch
Need for better handling of imaging data

25. 2. Reward Open Data

26. Methods
Answer
Metadata
softwareAnalysis
(Pipelines)
Workflows/
Environments
Idea
Study
Rewarding the
DOI, etc.
Publication
Publication
Publication
Data

27. Software
https://github.com/gigascience
Transparent
Open & able to build upon
Taking citeable snapshots
@jeejkang

28. gigagalaxy.net
Workflows
Reward Sharing of Workflows

29. Visualisations
& DOIs for workflows
http://www.gigasciencejournal.com/series/Galaxy 29

30. Facilitate reproducibility, reuse & sharing & publish outputs of:
Knitr, Sweave, Jupyter/iPython Notebook, etc.
Open Documents
Reward Open/Dynamic Workbooks

31. E.g.
http://www.gigasciencejournal.com/content/3/1/3

32. E.g.
http://www.gigasciencejournal.com/content/3/1/3

33. E.g.
http://www.gigasciencejournal.com/content/3/1/3
Reviewer (Christophe Pouzat):
“It took me a couple of hours to get the data, the few
custom developed routines, the “vignette” and to
REPRODUCE EXACTLY the analysis presented in the
manuscript. With few more hours, I was able to modify
the authors’ code to change their Fig. 4. In addition to
making the presented research trustworthy, the
reproducible research paradigm definitely makes the
reviewer’s job much more fun!

34. http://www.gigasciencejournal.com/content/3/1/23
http://www.gigasciencejournal.com/content/4/1/19
Virtual Machines
• Downloadable as virtual harddisk/available as Amazon Machine Image
• Experimenting & reviewing container (docker) submissions

35. Taking a microscope to the
publication process

36. http://biorxiv.org/content/early/2014/12/08/011973

37. Lessons Learned
• Is possible to push button(s) & recreate a result from
a paper
• Most published research findings are false. Or at
least have errors
• Reproducibility is COSTLY. How much are you willing
to spend?
• Much easier to do this before rather than after
publication

38. The cost of staying with the status quo?
• Ioannidis estimate that 85% of research resources are wasted.
• ~US$28B year unnecessarily spent on preclinical research in US.
• Each retraction estimated to cost $400,000.
http://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1001747
http://elifesciences.org/content/3/e02956
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002165

39. Death to the Publication. Long live the Research Object!
Manifesto for a reproducible publisher:
The era of the 1665-style publication is over
Reward replication not advertising
Credit FAIR data, not JIF-bait narrative
Granularity ≠ salami slicing. Ingelfinger is the enemy
We need a recognizable mark/badge/score(s) for replication
Separate category in ORCID for actually usable things
?

40. Ruibang Luo (BGI/HKU)
Shaoguang Liang (BGI-SZ)
Tin-Lap Lee (CUHK)
Qiong Luo (HKUST)
Senghong Wang (HKUST)
Yan Zhou (HKUST)
Thanks to:
@gigascience
facebook.com/GigaScience
blogs.biomedcentral.com/gigablog/
Peter Li
Chris Hunter
Jesse Si Zhe
Rob Davidson
Nicole Nogoy
Laurie Goodman
Amye Kenall (BMC)
Marco Roos (LUMC)
Mark Thompson (LUMC)
Jun Zhao (Lancaster)
Susanna Sansone (Oxford)
Philippe Rocca-Serra (Oxford)
Alejandra Gonzalez-Beltran (Oxford)
www.gigadb.org
gigagalaxy.net
www.gigasciencejournal.com
CBIIT
Funding from:
Our collaborators:team: (Case study)
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