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GigaScience
Laurie Goodman, PhD
Editor-in-Chief, GigaScience
ORCID ID: 0000-0001-9724-5976
Twitter: @GigaScience
Beyond the Narrative
Journal and Database
for ‘Big Data’ Research
in the Life and Medical Sciences
Editor-in-Chief: Laurie Goodman
Executive Editor: Scott Edmunds
Editor: Nicole Nogoy
Assistant Editor: Hans Zauner
GigaDB: Chris Hunter, Jesse Xiao
GigaGalaxy: Peter Li
in partnership with
What goes into research?
+ Area of Interest/
Question
Data & Metadata Collection
Analysis/Hypothesis/Analysis
Conclusions
What goes into a research article?
Analysis/Hypothesis/Analysis
Conclusions
+ Area of Interest/
Question
Data & Metadata Collection
Scientific Communication Via Publication
Scholarly articles are merely advertisement of scholarship.
The actual scholarly artefacts, i.e. the
data and computational methods, which
support the scholarship, remain largely
inaccessible
--- Jon B. Buckheit and David L. Donoho, WaveLaband reproducible research, 1995
Communicating Science
3 ½ Centuries of Publishing
Nature 1869 Nature 2014First Academic Journal 1665
The only significant change: Going from a paper to an electronic format (plus supplements — that can’t be searched…)
Moving Beyond the Narrative
Making everything underlying the Narrative available
Why Create a New Article
• Improves Reproducibility• Increases Transparency• Improves quality of presentation• Improves ability to reuse and
build on previous studies• The technology is (and has been)
available to do this
Introduction to GigaScience• Life science journal with a focus on “big data” studies
• Article types include research articles, data notes, technical notes, reviews, commentary, and editorials
• Have linked database GigaDB that hosts all data types
• Have linked source code-sharing (GigaGithub) and computational platforms (GigaGalaxy)
• We publish VMs, BioBoxes, etc
• We partner with organizations that have platforms to host citable detailed methods (Protocols.io) and open named review reports (Publons).
• Have in-house biocurators and data scientists to aid researchers
GigaSolution: deconstructing the paper
Publishing all the pieces:
• Data/software available
• Metadata/curation
• Interoperability
• Availability of workflows
• Transparent analyses
Data
Metadata
MethodsAnalyses
2012 Model of GigaScience Article
Data Sets inGigaDB
Analyses inGigaGalaxy
Paper inGigaScience
Open-access journal Data Publishing Platform
Data Analysis Platform
First Step: Linking Data To Articles
Data Sets inGigaDB
Paper inGigaScience
Linked to
Open-access journal Data Publishing Platform
Linking Data To Article
APC covers storage in GigaDB
Make it easy to cite
See where it got cited
Brief description of the data
Downloadable Files that include a readme and are organized, curated, and under a CC0 waiver
Paper DOI
Data set DOI
Linking papers and databy citation via DOIs
For Example:The Darwin Finch Data has been cited 14x.
…And more
That’s higher than most articles
Transparency and Reuse Needs Much More
• Data: GigaDB
• Software: Github
• Workflows– Galaxy
– Executable Docs
– VMs
• Images: OMERO
• Cloud storage, tools, and compute power…• Need this to reach the smaller
labs
github.com/gigascience/gigadb-cogini
More Journals have or are starting to introduce these and other tools: More is needed…
Research Objects: a concept & model
http://www.researchobject.org/
• Supporting publication of more than just PDFs, making data, code, & other resources first class citizens of scholarship.
• Recognizing that there is often a need to publish collections of these resources together as one shareable, cite-able resource.
• Enriching these resources and collections with any & all additional information required to make research reusable, & reproducible!
Built in to Our Publishing System and Partnerships
http://gigasciencejournal.com/blog/shortcut-from-biorxiv-to-gigascience /
Now with bioRxiv integration
GigaScience embraces
Publons + AcademicKarma = credit for reviewers efforts
http://publons.com/
Credit transparency/open peer review
http://academickarma.org/
gigagalaxy.net
Workflows
Reward Sharing of Workflows
http://www.gigasciencejournal.com/content/3/1/23http://www.gigasciencejournal.com/content/4/1/19
Virtual Machines/containers
• Downloadable as virtual harddisk/available as Amazon Machine Image
• Now publishing container (docker) submissions
First journal with deep integration with
Launched 2nd June 2016
Reward better handling of “wet” protocols…
• Create, share, modify forkeable protocols in repo.
• Download & run on smartphone app.
• Get discoverability, credit, DOIs for sharing methods.
• Create your own, or let us set up & you claim.
http://protocols.io/
https://codeocean.com/
New Integration: Code Ocean
Cloud-based executable research platform
Browse, share & run code on AWS
Creates compute capsule: encapsulation of the data, code, and computation environment
Integration into the paper, share via DOIs
First examples just published in GigaScience
Integrated plugin into GigaDB
Share your code this way!
Currently For a Researcher… it feels like this…
Well……because it is like this
Creating an integrated but separate environment via journals embracing the research object model; developing easy to use tools for authors and readers, and developing partnerships with organizations that already have tools will allow us to create the future article now.
Thanks to:Scott Edmunds, Executive Editor
Nicole Nogoy, EditorHans Zauner, Assistant Editor
Peter Li, Lead Data Manager
Chris Armit, Data Scientist
Chris Hunter, Lead BioCurator
Xiao (Jesse) Si Zhe, Database DeveloperMary Ann Tuli, Data Editor
[email protected]@gigasciencejournal.com
Contact us:
Follow us:
www.gigasciencel.comwww.gigadb.org and
@GigaSciencefacebook.com/GigaScience
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