The document discusses the challenges of urgent research needs around climate change and disease pandemics. It proposes that scientific publishing needs to change to better disseminate information openly and quickly in a trusted peer-reviewed form, while also sharing underlying data and methods. A new open-access journal called GigaByte is presented that uses an XML-based publishing platform to allow dynamic and machine-readable publication of research in an effort to address these challenges. Key features include streamlined review and publication processes, as well as embedding interactive content and using persistent identifiers.

1. Demonstrating bringing publications to life via
an End-to-end XML publishing platform
0000-0001-6444-1436
@SCEdmunds
scott@gigasciencejournal.com

2. Urgent challenges research needs to address
Climate change Disease pandemics (e.g. COVID19)
https://www.nytimes.com/2019/02/28/learning/teach-about-climate-change-with-these-24-new-york-times-graphs.html
https://www.nytimes.com/interactive/2020/03/21/upshot/coronavirus-deaths-by-country.html

3. Urgent challenges research needs to address
• Need to disseminate & communicate information openly to
global community
• Need to share this quickly and in a trusted form (peer reviewed)
• Research data, software and underlying methods and results
need to be shared for scrutiny and re-use
• Needs to be understandable by policy makers, public
Publishing to
the rescue?

4. Urgent challenges research needs to address
• Need to disseminate & communicate information openly to
global community
• Expensive. Held back by paywalls, APCs, and other barriers
• Need to share this quickly and in a trusted form (peer reviewed)
• Laborious, archaic tech, and untransparent processes
• Research data, software and underlying methods and results
need to be shared for scrutiny and re-use
• Hard work and little incentive to share
• Needs to be understandable by policy makers, public
• Barriers of language, jargon, and lack of interaction
Publishing to
the rescue?

5. Attempt to address this: GigaScience + GigaDB (2012)
http://gigadb.org/http://gigasciencejournal.com

6. 8years
in numbers
765
papers
published
5,411authors
from
78 countries
1,575
institutions
We’ve published
46 TB of data
1,914datasets
327,658files
5editors in
locations
across5
16time
zones
68+ years of editorial
experience
3data curators with
years of experience65+
20+
patents
and policy
documents
1,000+news articles
and blogs
Our contents is used in
21,186+tweets
PROSE
Award1
innovation in
journal publishing
multidisciplinary
231
Data
Notes
&
Lessons learned to date…

7. Lessons learned:
Tech really the bottleneck
Process much too slow &
expensive
Much too focused on narrative
and static “version of record”

8. D ATA C O D E E N T I T I E S FA C T S S TA B I L I T Y
A new approach
Follow the Software
Paradigm?
C O D E R E L E A S E F O R K U P D A T E R E P E A T
Deconstruct the “Version
of Record”?

9. Move to new XML end-to-end pipeline
Custom end-to-end workflow makes integrations simpler with one integration point

10. Features of new journal:
Main advantage of workflow is XML from start to end
https://gigabytejournal.com/
Several modules acting as one platform: no
import/export of files, so fast and accurate
Cutting out production allows huge time & cost saving
(currently 4-8 hours per paper)
Any number of versions can be published instantly,
including updates/forks
Leverage embeddable dynamic content (widgets)

11. Thinking about users: authors, reviewers, readers
https://gigabytejournal.com/
Streamlined questionnaire-based review
Reconfigured for short, easy to write & review data & software papers
Export as PDF, XML, HTML… “on the fly”

12. Focusing beyond VoR allows different views…
12

13. Thinking about readers: interactive features
13

14. https://www.thingiverse.com/thing:4579332
https://sketchfab.com/GigaDB/collections/microct-images-of-globigerina-bulloides-fossils
Interaction: increasing understanding & trust

15. https://doi.org/10.46471/gigabyte.6
Thinking about users: machines
High quality rich machine readable XML & APIs
Open (CC-BY) licensed, open citations, open corpus
Structured schema.org metadata
No hiding of material in supplemental files
Maximise use of persistent identifiers (PIDs)

16. https://doi.org/10.46471/gigabyte.6
Thinking about users: machines
High quality rich XML
CC-BY open licensed, open citations, open corpus
Structured schema.org metadata
No hiding of material in supplemental files
Maximise use of persistent identifiers (PIDs)
Who
ORCID IDs
CASRAI contributorship
Funder (Fundref)
Institution (ROR)
What
Species (NCBI, fishbase)
Cell/strain (RRID)
How
Equipment (RRID)
Software (RRID, bio.tools)
Output
Data (accessions, DOIs)
Results (DOIs)

17. A new approach with new tech
• Need to think differently to tackle urgent world problems
• Need to be completely open, transparent and FAIR
• Rethink “Version of Record”: focus on facts/data & discard the
packaging
• Follow the software paradigm, bring your research to life
• XML only workflow cuts time and cost to publish
Help us change scientific publishing, contact: editorial@gigabytejournal.com or submit
via http://gigabytejournal.com/
https://gigabytejournal.com/
Submit now, free APCs till 28th Feb 2021

18. Thanks to:
Laurie Goodman, Publisher
Nicole Nogoy, Editor
Hans Zauner, Assistant Editor
Hongling Zhao, Assistant Editor
Peter Li, Head of IT
Chris Hunter, Lead BioCurator
Chris Armit, Data Scientist
Mary Ann Tulli, Data Editor
Rija Ménagé, Senior Software Engineer
Ken Cho, Systems Programmer Analyst
Chen Qi, Shenzhen Office.
Follow us:
https://gigabytejournal.com/
Submit now, free APCs till 28th Feb 2021
@GigaByteJournal
facebook.com/GigaByteJournal
http://gigasciencejournal.com/blog/
editorial@gigabytejournal.com