GigaScience Beyond the Narrative Laurie Goodman, PhD - - PowerPoint PPT Presentation

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

• f 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, WaveLab

and reproducible research, 1995

Communicating Science

3 ½ Centuries of Publishing

Nature 1869 Nature 2014 First 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

Methods Analyses

2012 Model of GigaScience Article

Data Sets in GigaDB Analyses in GigaGalaxy Paper in GigaScience

Open-access journal Data Publishing Platform Data Analysis Platform

First Step: Linking Data To Articles

Data Sets in GigaDB

Paper in GigaScience 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

• f 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 data by 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
• f 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/3/1/23 http://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

• rganizations that

already have tools will allow us to create the future article now.

Thanks to:

Scott Edmunds, Executive Editor Nicole Nogoy, Editor

Hans Zauner, Assistant Editor

Peter Li, Lead Data Manager Chris Armit, Data Scientist Chris Hunter, Lead BioCurator Xiao (Jesse) Si Zhe, Database Developer

Mary Ann Tuli, Data Editor editorial@gigasciencejournal.com database@gigasciencejournal.com

Contact us: Follow us:

www.gigasciencel.com www.gigadb.org and @GigaScience facebook.com/GigaScience Sina Weibo: GigaScienceJournal Youku: http://i.youku.com/GigaScienceJournal QQ group: 71714580 WeChat: GigaScience Twitter: Facebook: