1. Introduction to GigaScience journal & database Chris I Hunter & Rob L Davidson ISI CODATA International Training Workshop on Big Data 11 th March 2015 DOI: 10.6084/m9.figshare.1330195

2. Biocurator responsible for content of GigaDB www.linkedin.com/profile/view? id=33608423 Chris Hunter Data analyst / developer responsible for tool development at GigaScience hk.linkedin.com/in/rldavidson Rob Davidson DOI: 10.6084/m9.figshare.1330195

3. THE PUBLISHING TRADITION DOI: 10.6084/m9.figshare.1330195

4. The publishing tradition 1812 16651869 DOI: 10.6084/m9.figshare.1330195

5. 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.1330195

6. The publishing tradition 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 DOI: 10.6084/m9.figshare.1330195

7. THE REPRODUCIBILITY CRISIS DOI: 10.6084/m9.figshare.1330195

8. 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.1330195

9. 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 9 DOI: 10.1038/ng.295 DOI: 10.6084/m9.figshare.1330195

10. 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.1330195

11. Supported by gov policy: e.g. UK and NIH MetaboLights repository  www.ebi.ac.uk/metabolights/ NIH Metabolomics Data Repository  www.metabolomicsworkbench.org/data/index.php ISA-Tab for metadata  http://www.isa-tools.org/format.html Data sharing – is beginning DOI: 10.6084/m9.figshare.1330195

12. What about methods? 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.1330195

13. Problem There is a reproducibility crisis  Researcher’s time is wasted  Research is a waste of public money (85%)  Published results are untrustworthy What's the solution?  Share data AND methods  Open AND transparent DOI: 10.6084/m9.figshare.1330195

14. GIGASCIENCE – JOURNAL, DATA, ANALYTICS DOI: 10.6084/m9.figshare.1330195

15. Introduction to GigaScience BGI – data producer BioMedCentral – open access publisher Open Data publication All ‘research objects’ are ‘data’ Online format Beyond ‘dead trees’ DOI: 10.6084/m9.figshare.1330195

16. Anatomy of a traditional Publication Data Idea Study Analysis Answer Metadata 16 DOI: 10.6084/m9.figshare.1330195

17. Anatomy of a Data Publication 17 Data Idea Study Analysis Answer Metadata DOI: 10.6084/m9.figshare.1330195

18. Multi-faceted publication Open-access journal Data Publishing Platform Data Analysis Platform Data Metadata Methods Analyses DOI: 10.6084/m9.figshare.1330195

19. “Deconstructed” Journal “Regular” Journal “Conscientious” Online Journal 19 DOI: 10.6084/m9.figshare.1330195

20. “Deconstructed” Journal “Regular” Journal “Conscientious” Online Journal 20 DOI: 10.6084/m9.figshare.1330195

21. “Deconstructed” Journal “Regular” Journal “Conscientious” Online Journal 21 DOI: 10.6084/m9.figshare.1330195

22. Image Source: http://commons.wikimedia.org/wiki/File:System-Mechanic-California.jpg “Deconstructed” Journal “Regular” Journal “Conscientious” Online Journal 22 DOI: 10.6084/m9.figshare.1330195

23. BENEFITS OF SHARING DOI: 10.6084/m9.figshare.1330195

24. Potential benefits collaboration and enhanced outcomes better education and research training new opportunities and uses a more complete and transparent record of ‘science’ potentially more sensitive and less invasive research evaluation greater visibility and reward Article: http://bit.ly/1AdDVh8 DOI: 10.6084/m9.figshare.1330195

25. Sharing aids authors… Sharing Detailed Research Data Is Associated with Increased Citation Rate. DOI: 10.1371/journal.pone.0000308 DOI: 10.6084/m9.figshare.1330195

26. Data Sharing Good for the field Genomics/Bioinformatics Long term sharing infrastructure: Strong use of standards/policies: DOI: 10.6084/m9.figshare.1330195

27. IRRI GALAXY Data sharing: good for the field Rice 3K project: 3,000 rice genomes, 13.4TB public data DOI: 10.6084/m9.figshare.1330195

28. IRRI GALAXY Data sharing: good for the field Rice 3K project: 3,000 rice genomes, 13.4TB public data DOI: 10.6084/m9.figshare.1330195

29. OPEN PEER REVIEW DOI: 10.6084/m9.figshare.1330195

30. More transparency: open peer review DOI: 10.1186/2047-217X-2-1 DOI: 10.6084/m9.figshare.1330195

31. Credit for review Comments on GigaScience site Publons – Record/verify reviews – Showcase/credit – Enhanced discussion Academic karma – Record – Review more interesting work – Showcase DOI: 10.6084/m9.figshare.1330195

32. @gigascience facebook.com/GigaScience Scott Edmunds Peter Li Chris Hunter Rob Davidson Jesse Si Zhe Nicole Nogoy Laurie Goodman Amye Kenall (BMC) www.gigadb.org galaxy.cbiit.cuhk.edu.hk www.gigasciencejournal.com blogs.biomedcentral.com/gigablog/ DOI: 10.6084/m9.figshare.1330195