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

GigaScience Beyond the Narrative Laurie Goodman, PhD Editor-in-Chief, GigaScience Laurie@gigasciencejournal.com ORCID ID: 0000-0001-9724-5976 Twitter: @GigaScience

Journal and Database f or ‘Big Data’ Research in the Life and Medical Sciences in partnership with Editor-in-Chief : Laurie Goodman Executive Editor : Scott Edmunds Editor : Nicole Nogoy Assistant Editor : Hans Zauner GigaDB: Chris Hunter, Jesse Xiao GigaGalaxy: Peter Li

What goes into research? + Area of Interest/ Question Data & Metadata Collection Analysis/Hypothesis/Analysis Conclusions

What goes into a research article ? + Area of Interest/ Question Data & Metadata Collection Analysis/Hypothesis/Analysis Conclusions

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, WaveLab and reproducible research, 1995

Communicating Science 3 ½ Centuries of Publishing The only significant change: Going from a paper to an electronic format (plus supplements — that can’t be searched…) Nature 2014 Nature 1869 First Academic Journal 1665

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 Analyses • Metadata/curation Methods • Interoperability Metadata Data • Availability of workflows • Transparent analyses

2012 Model of GigaScience Article Data Publishing Platform Open-access journal Data Sets in Giga DB Analyses in Giga Galaxy Paper in GigaScience Data Analysis Platform

First Step: Linking Data To Articles Data Publishing Platform Open-access journal Linked to Data Sets in Paper in Giga DB GigaScience

Linking Data To Article APC covers storage in GigaDB

Brief Make it easy to cite description of the data See where it got cited Downloadable Files that include a readme and are organized, curated, and under a CC0 waiver

Linking papers and data by citation via DOIs Data set DOI Paper DOI

For Example: The Darwin Finch Data has been cited 14x. That’s higher than most articles … And more

Transparency and Reuse Needs Much More • Data: GigaDB • Software: Github github.com/gigascience/gigadb-cogini • Workflows – Galaxy – Executable Docs – VMs • Images: OMERO • Cloud storage, tools, and compute power… • Need this to reach the smaller labs More Journals have or are starting to introduce these and other tools: More is needed…

Research Objects: a concept & model • 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! http://www.researchobject.org/

Built in to Our Publishing System and Partnerships

GigaScience embraces Now with bioRxiv integration http://gigasciencejournal.com/blog/shortcut-from-biorxiv-to-gigascience /

Credit transparency/open peer review Publons + AcademicKarma = credit for reviewers efforts http://academickarma.org/ http://publons.com/

Workflows Reward Sharing of Workflows gigagalaxy.net

Virtual Machines/containers • Downloadable as virtual harddisk/available as Amazon Machine Image • Now publishing container (docker) submissions http://www.gigasciencejournal.com/content/3/1/23 http://www.gigasciencejournal.com/content/4/1/19

Reward better handling of “wet” protocols… First journal with deep integration with Launched 2 nd June 2016 • 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/

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! https://codeocean.com/

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 , 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 Contact us: editorial@gigasciencejournal.com database@gigasciencejournal.com Follow us: Twitter: @GigaScience Facebook: facebook.com/GigaScience Sina Weibo: GigaScienceJournal Youku: http://i.youku.com/GigaScienceJournal QQ group: 71714580 WeChat: GigaScience www.gigasciencel.com and www.gigadb.org