GigaScience EiC Laurie Goodman's talk at the Council of Science Editors Annual Meeting on "Open Access - Viewpoint of New Journal". 4th May 2014

1. Open Access
Viewpoint of New Journal
Laurie Goodman, PhD
Editor-in-Chief, GigaScience
Laurie@gigasciencejournal.com
ORCID ID: 0000-0001-9724-5976

2. Open Access
View from the Just-Launched
It is Expected
The End

3. Okay-
That’s actually only the Beginning
• Open Access serves as a foundation for a
specific way of thinking about scientific
communication and the role of journals and
publishers
• It is actually a step toward complete
transparency
• It is a step toward changing how we
communicate science — from start to finish

4. And it would be nice if established
journals did this too…
New Journals

5. New Journals as an Evolutionary Mechanism
• New journals are in a unique position to try new ideas and new
ways of doing things
• They MUST test new things
– Even ones that seem to fly in the face of long-held (and
sometimes treasured) views
• They MUST be ready to have things they try FAIL
• They MUST be ready to jettison what doesn’t work
– Even if that means changing midstream when a new and
better opportunity arises
• They MUST be responsive –both reactive and proactive
– Reactive is not evil: but it can be is if is the only activity way
of responding…
• They NEED their publishers to support and PROMOTE this

6. What we’re doing at GigaScience
1. Requiring all data supporting work to be Freely available in a
publically available repository
– How we’re promoting this:
• Journal-dedicated data and software repository GigaDB
that hosts ALL data types.
• Have a Biocurator(s) to aid in handling Metadata
• All Datasets are provided a Digital Object Identifier
(DOI) making them citable and countable (reward for
making data available- GigaDB is tracked by Thompson Reuters Data Citation Index)
• All Material in GigaDB is available under a CC0 Waiver
• Data with a publically approved database must be
submitted there as well
• Provide Direct links to all associated information

7. Citable
Links to ALL
associated
information To Come:
Grant information
and link
NOTE:
This data set is being
released PRIOR to the
publication of the
analysis paper
With downloadable
citation functionality
http://gigadb.org/

10. What we’re doing at GigaScience
Requiring all software and work to be Freely available in a
publically available repository
– How we’re promoting this:
• Journal-Dedicated repository GigaDB that hosts
software so it can be downloaded.
• Software and Workflows are provided a DOI making
them citable and countable (reward)
• Journal-dedicated Galaxy Platform to run tools
• Have a Data Manager and Data Scientist to wrap and
deploy software tools
• All software created by authors must be open-source

13. Soapdenovo2 Galaxy workflow

14. But wait- there’s more…
Going Beyond Access and Reproducibility
Targets:
Peer-Review
“Embargoes”
If we are in the business of Communicating
Then we should be
PROMOTING COMMUNICATION
ALL THE TIME

15. What we’re doing at GigaScience
Peer Review
• Reviews are signed (Other Journals are doing this)
– Currently Opt-Out. Planning to make it mandatory
• All Reviews (and all pre-publication history) are
available upon publication.

16. 8 referees downloaded & tested data, then signed reports
Reward open & transparent review

17. Post publication: bloggers pull apart code/reviews in blogs + wiki:
SOAPdenov2 wiki: http://homolog.us/wiki1/index.php?title=SOAPdenovo2
Homologus blogs: http://www.homolog.us/blogs/category/soapdenovo/
Reward open & transparent review

18. What we’re doing at GigaScience
“Embargoes” and “Confidentiality”
• Leave decisions of when to share to the researcher
but encourage early sharing
• Actively encourage the use of Pre-Print Servers
• Take Open-Access one step further
Consider EXTRA-OPEN Peer-Review
• Eliminate Press Embargoes

19. New & more transparent peer-
review: pre-prints
1. http://arxiv.org/abs/1305.6760
2. http://www.nature.com/news/preprints-come-to-life-1.14140
Preprints

20. New & more transparent peer-
review: pre-prints
PrePrints

21. Real-time open-review = paper in arXiv + blogged reviews
Reward open & transparent review
http://tmblr.co/ZzXdssfOMJfywww.gigasciencejournal.com/content/2/1/10
Real Time Peer Review

22. Real-time open-review = paper in arXiv + blogged reviews
Reward open & transparent review
Real-Time Peer Review

23. Current Scientific Communication
Research (shhhhh!)
Okay- talk at conferences…
--maybe preprints (but ASK)
Don’t talk to the press!
-Publication-
INFORMATION!!!
BIG PRESS RELEASE
WE FOUND THE CURE!!!!
Punctuated Science
Research (shhhhh!)
Okay- talk at conferences…
--maybe preprints (but ASK)
Don’t talk to the press!

24. Scientific Publication as part of a
Continuum of Scientific Communication
Scientific Research
Conferences
PreprintsPress Interviews
Public Discourse
Twitter
Interactive web tools
Collaboration
Shouting from the rooftops!!!
Blogs
Publication
Lets Promote Real-Time Science
Sharing Data
Sharing Tools
Indication that a stage of research has been
formally vetted and is available within easily
accessible and condensed format
Education

25. Thanks to:
editorial@gigasciencejournal.com
database@gigasciencejournal.com
@gigascience
facebook.com/GigaScience
blogs.openaccesscentral.com/blogs/gigablog/
Contact us:
Scott Edmunds, Executive Editor
Nicole Nogoy, Commissioning Editor
Peter Li, Lead Data Manager
Chris Hunter, Lead BioCurator
Rob Davidson, Data Scientist
Xiao (Jesse) Si Zhe, Database Developer
Amye Kenall, Journal Development Manager
Follow us:
www.gigasciencejournal.com
www.gigadb.org