GigaScience

Laurie Goodman, PhD

Editor-in-Chief, GigaScience

Laurie@gigasciencejournal.com

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

editorial@gigasciencejournal.comdatabase@gigasciencejournal.com

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