Scott Edmunds on a new publishing workflow for rapid dissemination of genomes using GigaByte & GigaDB. Presented at Biodiversity 2020 in the Annotation & Databases track, 9th October 2020.

1. A new publishing
workflow for rapid
dissemination of
genomes using
GigaByte & GigaDB
0000-0001-6444-1436
@SCEdmunds
scott@gigasciencejournal.com

2. Genome projects go planetary

3. Scaling up of the pipelines…
Sequencing Data Dissemination?

4. Attempt to address this: GigaScience + GigaDB (2012)
http://gigadb.org/
https://github.com/gigascience/gigadb-website/http://gigasciencejournal.com

5. 8years
in numbers
765
papers
published
5,411authors
from
78 countries
1,575
institutions
We’ve published
46 TB of data
1,914datasets (1221 genomic)
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
&
& many consortia

6. 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
Lessons learned:
Tech is terrible.
Process too slow, expensive,
static, narrative focused.

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

8. Features of new journal:
Main advantage of workflow is XML from start to end
Several modules acting as one platform: no import/export
of files, so fast and accurate
Cutting out production allows big time & cost saving
Any number of versions can be published instantly, including
typographic quality PDF or updates/forks
Allows instantaneous switch of views, language, fonts
(visually impaired/dyslexic, etc.)
Initial focus on forkable products: data + software + updates
Leverage embeddable dynamic content/widgets
Streamlined questionnaire-based review
https://gigabytejournal.com/

9. https://news.ucsc.edu/2010/11/genome10k.html
Orphaned for a decade, G10K Banjo frog is the first example in
https://gigabytejournal.com/articles/2

10. Thanks to:
Laurie Goodman, Publisher
Nicole Nogoy, Executive Editor
Hans Zauner, 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.
@GigaByteJournal
facebook.com/GigaByteJournal
http://gigasciencejournal.com/blog/
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