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Software Sustainability Institute There’s No Such Thing As Irreproducible Research 27.

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Presentation on theme: "Software Sustainability Institute There’s No Such Thing As Irreproducible Research 27."— Presentation transcript:

1 Software Sustainability Institute www.software.ac.uk There’s No Such Thing As Irreproducible Research http://dx.doi.org/10.6084/m9.figshare.2067747 27 th January 2016, Digging Into Data, Glasgow Neil Chue Hong (@npch), Software Sustainability Institute ORCID: 0000-0002-8876-7606 | N.ChueHong@software.ac.uk Slides licensed under CC-BY where indicated: Supported by Project funding from

2 Software Sustainability Institute www.software.ac.uk Or… “A personal journey as a data explorer” 10.6084/m9.figshare.2067747

3 Software Sustainability Institute www.software.ac.uk 10.6084/m9.figshare.2067747

4 Software Sustainability Institute www.software.ac.uk 10.6084/m9.figshare.2067747

5 Software Sustainability Institute www.software.ac.uk 10.6084/m9.figshare.2067747

6 Software Sustainability Institute www.software.ac.uk 10.6084/m9.figshare.2067747

7 Software Sustainability Institute www.software.ac.uk 10.6084/m9.figshare.2067747

8 Software Sustainability Institute www.software.ac.uk 10.6084/m9.figshare.2067747

9 Software Sustainability Institute www.software.ac.uk T T 10.6084/m9.figshare.2067747

10 Software Sustainability Institute www.software.ac.uk T T “Virtual data warehouse” 10.6084/m9.figshare.2067747

11 Software Sustainability Institute www.software.ac.uk T T Public Health Data - Name - Address - Visits - Symptoms - Treatments 10.6084/m9.figshare.2067747

12 Software Sustainability Institute www.software.ac.uk 10.6084/m9.figshare.2067747

13 Software Sustainability Institute www.software.ac.uk 10.6084/m9.figshare.2067747

14 Software Sustainability Institute www.software.ac.uk 10.6084/m9.figshare.2067747

15 Software Sustainability Institute www.software.ac.uk 10.6084/m9.figshare.2067747

16 Software Sustainability Institute www.software.ac.uk 10.6084/m9.figshare.2067747

17 Software Sustainability Institute www.software.ac.uk 10.6084/m9.figshare.2067747

18 Software Sustainability Institute www.software.ac.uk Mapping courtesy of Robin T Wilson 10.6084/m9.figshare.2067747

19 Software Sustainability Institute www.software.ac.uk T T This taught me three things… 10.6084/m9.figshare.2067747

20 Software Sustainability Institute www.software.ac.uk T T 1. The power of data is when it’s brought together 10.6084/m9.figshare.2067747

21 Software Sustainability Institute www.software.ac.uk T T 2. Software can help solve difficult data integration problems 10.6084/m9.figshare.2067747

22 Software Sustainability Institute www.software.ac.uk T T 3. No-one can spell diarhea diereah dyereeah diarrheah dioreah diarrhoea! 10.6084/m9.figshare.2067747

23 Software Sustainability Institute www.software.ac.uk Positive selection in large genomic datasets Selection at pleiotropic loci underlies disease co-occurrence in human populations. Navarro, Haley, Karosas et al. Submitted to Nature Genetics 10.6084/m9.figshare.2067747

24 Software Sustainability Institute www.software.ac.uk Hapbin: fast haplotype based scans hapbin: An Efficient Program for Performing Haplotype-Based Scans for Positive Selection in Large Genomic Datasets. DOI: 10.1093/molbev/msv172 10.6084/m9.figshare.2067747

25 Software Sustainability Institute www.software.ac.uk Open Source lets others benefit Slide courtesy of Nancy Wilkins-Diehr BEAST software licensed under LGPL 10.6084/m9.figshare.2067747

26 Software Sustainability Institute www.software.ac.uk 10.6084/m9.figshare.2067747

27 Software Sustainability Institute www.software.ac.uk Errors due to bioinformatics pipeline 10.6084/m9.figshare.2067747

28 Software Sustainability Institute www.software.ac.uk Raise standards for preclinical cancer research 47 out of 53 “landmark” publications could not be replicated Begley, Ellis. Nature, 483, 2012 doi:10.1038/483531a 10.6084/m9.figshare.2067747

29 Software Sustainability Institute www.software.ac.uk, it’ Victoria Stodden, AMP 2011 http://www.stodden.net/AMP2011/, Special Issue Reproducible Research Computing in Science and Engineering July/August 2012, 14(4) Howison and Herbsleb (2013) "Incentives and Integration In Scientific Software Production" CSCW 2013. 10.6084/m9.figshare.2067747

30 Software Sustainability Institute www.software.ac.uk Errors due to bioinformatics pipeline The results presented in the Report “Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent“ were affected by a bioinformatics error Llorente et al. Science, 350, 6262 doi:10.1126/science.aad2879 10.6084/m9.figshare.2067747

31 Software Sustainability Institute www.software.ac.uk T T Nullius in verba “Take nobody’s word for it” 10.6084/m9.figshare.2067747

32 Software Sustainability Institute www.software.ac.uk T T There’s no such thing as irreproducible research There’s reproducible research and there’s ignorance It’s not research if it’s not transparent 10.6084/m9.figshare.2067747

33 Software Sustainability Institute www.software.ac.uk

34 Software Sustainability Institute www.software.ac.uk ^ and Software 10.6084/m9.figshare.2067747

35 Software Sustainability Institute www.software.ac.uk T T 10.6084/m9.figshare.2067747

36 Software Sustainability Institute www.software.ac.uk T T Vandewalle (2012) DOI: 10.1109/MCSE.2012.63 10.6084/m9.figshare.2067747

37 Software Sustainability Institute www.software.ac.uk T T Without data it’s difficult to validate results. But without code, we waste the opportunity to advance science. 10.6084/m9.figshare.2067747

38 Software Sustainability Institute www.software.ac.uk Acknowledgements The SSI team: -Aleksandra Pawlik -Carole Goble -Claire Wyatt -Clem Hadfield -Dave De Roure -Devasena Prasad -Giacomo Peru -Graeme Smith -Iain Emsley -John Robinson -Les Carr -Mario Antonioletti -Mark Parsons -Mike Jackson -Olivier Philippe -Shoaib Sufi -Simon Hettrick -Stephen Crouch The SSI Fellows and collaborators especially: -James Baker -James Hetherington -Martin Hammitzsch -Robin Wilson (for contributing examples) EPCC Industry Projects: -Mark Sawyer -Maureen Wilkinson -Paul Graham -Rob Baxter -Terry Sloan Mouse Atlas: -James Sharpe -Richard Baldock Epigenetic analysis - James Prendergast - Colin Maclean Scientific software: -Dan Katz -Heather Piowowar -James Howison -Jeff Carver -Jennifer Schopf -Kaitlin Thaney -Martin Fenner -Victoria Stodden Software/Data Carpentry -Greg Wilson -Jonah Duckles -Katy Huff -Tracy Teal Slides at: http://dx.doi.org/10.6084/m9.figshare.2067747

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