Presentation is loading. Please wait.

Presentation is loading. Please wait.

WHAT ARE WE GOING TO DO WITH DATA? Rob L Davidson #WCSJ2015 This presentation DOI:10.6084/m9.figshare.1439750.

Published byEustace Chambers Modified over 9 years ago

Similar presentations

Presentation on theme: "WHAT ARE WE GOING TO DO WITH DATA? Rob L Davidson #WCSJ2015 This presentation DOI:10.6084/m9.figshare.1439750."— Presentation transcript:

1 WHAT ARE WE GOING TO DO WITH DATA? Rob L Davidson GigaScience @bobbledavidson #WCSJ2015 This presentation DOI:10.6084/m9.figshare.1439750

2 Up ahead The need for Open Data in science GigaScience and GigaDB Everything is data Open is accessible Literate programming So, what are we going to do with data? DOI:10.6084/m9.figshare.1439750

3 THE NEED FOR OPEN DATA IN SCIENCE DOI:10.6084/m9.figshare.1439750

4 Researcher bias Positive result bias  20 teams do studies, 1 publishes p<0.05 Poorly explained analyses DOI: 10.1371/journal.pmed.0020124 DOI:10.6084/m9.figshare.1439750

5 Problem: Reproducibility Out of 18 microarray papers, results from 10 could not be reproduced Out of 18 microarray papers, results from 10 could not be reproduced 5 DOI: 10.1038/ng.295 DOI:10.6084/m9.figshare.1439750

6 Software? http://reproducibility.cs.arizona.edu/ “The good news is that I was able to find some code. I am just hoping that it is a stable working version of the code... I have lost some data... The bad news is that the code is not commented and/or clean. So, I cannot really guarantee that you will enjoy playing with it.” 613 papers tested 123 successful reproductions DOI:10.6084/m9.figshare.1439750

7 DOI: 10.1371/journal.pmed.1001747 85% of research resources are wasted! We must... favor... unbiased, transparent, collaborative research with greater standardization Share data, protocols, materials, software, other tools DOI:10.6084/m9.figshare.1439750

8 What, why Open Data? Knowledge is open if anyone is – free to access, – use, – modify, – and share it – subject, at most, to measures that preserve provenance and openness. http://opendefinition.org/od/ DOI:10.6084/m9.figshare.1439750

9 FAIR Data http://datafairport.org/ DOI:10.6084/m9.figshare.1439750

10 GIGASCIENCE AND GIGADB DOI:10.6084/m9.figshare.1439750

11 The publishing tradition 1812 16651869 DOI:10.6084/m9.figshare.1439750

12 The publishing tradition Aimed at paper product Limited length Limited detail No supporting data No supporting code Poor images Limited figures DOI:10.6084/m9.figshare.1439750

13 Anatomy of a traditional Publication Data Idea Study Analysis Answer Metadata 13 DOI:10.6084/m9.figshare.1439750

14 Anatomy of an Open Data Publication 14 Data Idea Study Analysis Answer Metadata DOI:10.6084/m9.figshare.1439750

15 Multi-faceted publication Open-access journal Data Publishing Platform Data Analysis Platform Data Metadata Methods Analyses DOI:10.6084/m9.figshare.1439750

16 “Deconstructed” Journal “Regular” Journal “Conscientious” Online Journal 16 DOI:10.6084/m9.figshare.1439750

17 “Deconstructed” Journal “Regular” Journal “Conscientious” Online Journal 17 DOI:10.6084/m9.figshare.1439750

18 “Deconstructed” Journal “Regular” Journal “Conscientious” Online Journal 18 DOI:10.6084/m9.figshare.1439750

19 Image Source: http://commons.wikimedia.org/wiki/File:System-Mechanic-California.jpg “Deconstructed” Journal “Regular” Journal “Conscientious” Online Journal 19 DOI:10.6084/m9.figshare.1439750

20 EVERYTHING IS DATA DOI:10.6084/m9.figshare.1439750

21 Data is data DOI:10.1186/2047-217X-3-7 DOI:10.6084/m9.figshare.1439750

22 Software is data “For loading data from the provided datasets, a script that can load individual spectra or images is provided” DOI: DOI:10.6084/m9.figshare.1439750

23 Metadata is data Findable, reusable… Bioontologies/ISA-Tab – Standard language ORCID – Unique, traceable authors Fundref – Track funding outputs API’s – Easy search DOI:10.6084/m9.figshare.1439750

24 ACCESSIBLE, USABLE DATA DOI:10.6084/m9.figshare.1439750

25 Curation Not all science data is pretty ISA-Tab, SRA helps Peer reviewed data is better data http://bit.ly/1F47YZz DOI:10.6084/m9.figshare.1439750

26 Software pipelines Gigagalaxy.net Tool List Tool Parameters History/results DOI:10.6084/m9.figshare.1439750

27 Visualise pipelines DOI:10.6084/m9.figshare.1439750 Gigagalaxy.net

28 Reproducing results? SOAPdenovo2 S. aureus pipeline DOI: 10.1186/2047-217X-1-18 DOI:10.6084/m9.figshare.1439750

29 Easy installation Virtual machine – Pre-installed – Peer-reviewed – Reproducibility, frozen in time DOI:10.1186/2047-217X-3-23 DOI:10.6084/m9.figshare.1439750

30 Literate programming Data journalism for all! KnitR, iPython, project Jupyter DOI:10.1186/2047-217X-3-3 DOI:10.6084/m9.figshare.1439750

31 WHAT ARE WE GOING TO DO WITH DATA? DOI:10.6084/m9.figshare.1439750

32 Add value http://bit.ly/1JyTfxO DOI:10.6084/m9.figshare.1439750

33 Do science? Data – DOI: 10.5524/100034 Subsequent analysis – DOI: 10.1126/scitranslmed.3006086 Science journalism – http://bit.ly/1AXEkKJ Why not do part 2 as well? DOI:10.6084/m9.figshare.1439750

34 Summary Science has problems – so how good can science journalism be? Things are changing – slowly The future is bright The future is data-driven Data journalists will be the new scientists? DOI:10.6084/m9.figshare.1439750

35 THANKS! DOI:10.6084/m9.figshare.1439750 GigaScience team: Scott Edmunds Peter Li Chris Hunter Jesse Xiao Rob Davidson

Download ppt "WHAT ARE WE GOING TO DO WITH DATA? Rob L Davidson #WCSJ2015 This presentation DOI:10.6084/m9.figshare.1439750."

Similar presentations

Goals Rob Procter Dave Berry Anne Trefethen Paul Watson.

Goals Rob Procter Dave Berry Anne Trefethen Paul Watson.
Software workflows as research objects & GigaGalaxy Rob L Davidson, Chris I Hunter ISI CODATA International Training Workshop on Big Data 11 th March 2015.

Software workflows as research objects & GigaGalaxy Rob L Davidson, Chris I Hunter ISI CODATA International Training Workshop on Big Data 11 th March 2015.
Rewarding Reproducibility and Method Publishing the GigaScience Way Scott Edmunds

Rewarding Reproducibility and Method Publishing the GigaScience Way Scott Edmunds
Journals Full Text Resources Including MedIND. For Scholarly Information We start with Bibliographic Databases having references to journals and other.

Journals Full Text Resources Including MedIND. For Scholarly Information We start with Bibliographic Databases having references to journals and other.
Andy Nicholls – Head of Consultancy DevelopR – formalising R Development.

Andy Nicholls – Head of Consultancy DevelopR – formalising R Development.
Data Publishing Workflows: Strategies and Standards

Data Publishing Workflows: Strategies and Standards
Knowledge and solutions for a changing world Adventures in computational reproducible research for ribosomal based community profiling Dave Beck

Knowledge and solutions for a changing world Adventures in computational reproducible research for ribosomal based community profiling Dave Beck
FROM DATA REPOSITORIES TO DATA JOURNALS – WHERE, WHEN AND HOW TO SUBMIT Andrew L. Hufton Managing Editor, Scientific Data Nature Publishing Group

FROM DATA REPOSITORIES TO DATA JOURNALS – WHERE, WHEN AND HOW TO SUBMIT Andrew L. Hufton Managing Editor, Scientific Data Nature Publishing Group
The iPlant Collaborative Community Cyberinfrastructure for Life Science Tools and Services Workshop Discovery Environment Overview.

The iPlant Collaborative Community Cyberinfrastructure for Life Science Tools and Services Workshop Discovery Environment Overview.
INTRODUCTION TO RESEARCH DATA MANAGEMENT Robin Desmeules Janice Kung J W Scott Health Sciences Library University of Alberta Libraries.

INTRODUCTION TO RESEARCH DATA MANAGEMENT Robin Desmeules Janice Kung J W Scott Health Sciences Library University of Alberta Libraries.
Software workflows as research objects Rob L Davidson, Chris I Hunter ISI CODATA International Training Workshop on Big Data 11 th March 2015 Slideshow-URL.

Software workflows as research objects Rob L Davidson, Chris I Hunter ISI CODATA International Training Workshop on Big Data 11 th March 2015 Slideshow-URL.
Publishing and crediting different shaped research objects the way Scott Edmunds, #FORCE2015.

Publishing and crediting different shaped research objects the way Scott Edmunds, #FORCE2015.
Promoting data dissemination and reproducibility. Christopher I. Hunter, Scott C. Edmunds, Peter Li, Xiao Si Zhe, Robert L Davidson, Laurie Goodman. Submit.

Promoting data dissemination and reproducibility. Christopher I. Hunter, Scott C. Edmunds, Peter Li, Xiao Si Zhe, Robert L Davidson, Laurie Goodman. Submit.
Tools for reproducible and accessible science VMs, KnitR and OMERO Rob Davidson Cardiac Physiome Workshop Auckland, April 8th 2015.

Tools for reproducible and accessible science VMs, KnitR and OMERO Rob Davidson Cardiac Physiome Workshop Auckland, April 8th 2015.
Open Data, Open Source: preparing for Big Data in Metabolomics Rob L Davidson #MetSoc2015 This presentation DOI:10.6084/m9.figshare.1439750.

Open Data, Open Source: preparing for Big Data in Metabolomics Rob L Davidson #MetSoc2015 This presentation DOI: /m9.figshare
Tools for reproducible and accessible science KnitR, VMs and OMERO Rob Davidson Cardiac Physiome Workshop Auckland, April 8th 2015 DOI for this talk: 10.6084/m9.figshare.1368774.

Tools for reproducible and accessible science KnitR, VMs and OMERO Rob Davidson Cardiac Physiome Workshop Auckland, April 8th 2015 DOI for this talk: /m9.figshare
DATAVERSE FOR JOURNALS Mercè Crosas, Ph.D. Director of Data Science IQSS, Harvard Society for Scholarly Publishing 37 th Meeting,

DATAVERSE FOR JOURNALS Mercè Crosas, Ph.D. Director of Data Science IQSS, Harvard Society for Scholarly Publishing 37 th Meeting,
Data Citation: the next big thing… ?!?! 1 Victoria University 20 Nov. 2014.

Data Citation: the next big thing… ?!?! 1 Victoria University 20 Nov
Open Data, Open Source: preparing for Big Data in Metabolomics Rob L Davidson #MetSoc2015 This presentation DOI: 10.6084/m9.figshare.1466889.

Open Data, Open Source: preparing for Big Data in Metabolomics Rob L Davidson #MetSoc2015 This presentation DOI: /m9.figshare
Software workflows as research objects & GigaGalaxy Rob L Davidson, Chris I Hunter ISI CODATA International Training Workshop on Big Data 11 th March 2015.

Software workflows as research objects & GigaGalaxy Rob L Davidson, Chris I Hunter ISI CODATA International Training Workshop on Big Data 11 th March 2015.

Similar presentations

Ads by Google