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Reproducibility (and the R*) of Science: motivations, challenges and trends

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IRCDL Pisa 31 Jan – 1 Feb 2019
https://ircdl2019.isti.cnr.it/,
IRCDL 2019 15th Italian Research Conference on Digital Libraries.

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Reproducibility (and the R*) of Science: motivations, challenges and trends

  1. 1. Reproducibility (and the R*) of Science: motivations, challenges and trends Professor Carole Goble The University of Manchester, UK Software Sustainability Institute, UK Head of Node ELIXIR-UK ELIXIR, IBISBA, FAIRDOM Association e.V., BioExcel Life Science Infrastructures carole.goble@manchester.ac.uk IRCDL Pisa 31 Jan – 1 Feb 2019 Beware. Results may vary.
  2. 2. Reproducibility of Science… A fundamental given of the Scientific Method…. https://xkcd.com/242/
  3. 3. Reproducibility on the Agenda
  4. 4. The famous Nature survey 1576 researchers, 2016 https://www.nature.com/news/1-500-scientists-lift-the-lid-on-reproducibility-1.19970
  5. 5. Reporting and Availability John P. A. Ioannidis Why Most Published Research FindingsAre False, August 30, 2005, DOI: 10.1371/journal.pmed.0020124 incomplete reporting of method, software configurations, resources, parameters & resource versions, missed steps, missing data, vague methods, missing software, unreproducible environments. Joppa, et al,TroublingTrends in Scientific Software Use SCIENCE 340 May 2013 BetterTraining Methodological Support More robust designs Independent accountability Collaboration & team science Diversifying peer review Better Practices Funding replication studies Rewarding right behaviour Design Flaws HARKIng (hypothesizing after the results are known), cherry picking data, random seed reporting, non-independent bias, poor positive and negative controls, poor normalisation, arbitrary cut-offs, premature data triage, un-validated materials, improper statistical analysis, poor statistical power, stop when “get to the right answer”, software misconfigurations, misapplied black box software
  6. 6. Trend: Policy and advice proliferation Findable ( and be Citable) Accessible (and beTrackable) Interoperable (and be Intelligible) Reusable (and be Reproducible) Record, Automate, Contain, Access
  7. 7. *Based on Scientific publications • announce a result • convince readers to trust it. Experimental science • describe the results • provide a clear enough the materials and protocol to allow successful repetition and extension. (Jill Mesirov 2010*) Computational science • describe the results • provide the complete software development environment, data, instructions, techniques (which generated the figures) (David Donoho 1995*).
  8. 8. “Virtual Witnessing” *Leviathan and theAir-Pump: Hobbes, Boyle, and the Experimental Life (1985) Shapin and Schaffer.Joseph Wright, Experiment with the Air Pump c. 1768
  9. 9. “virtually witnessing” the “moist lab” Experiment Setup Methods Algorithms, spec. of the analysis steps, models… Materials Datasets, parameters, algorithm seeds… Instruments Codes, services, scripts, workflows, reference datasets… Laboratory Software and hardware infrastructure… Wet Dry Physical Lab Chemicals, reagents, samples, strain of mouse… Mass specs, sequencers, microscopes, calibrations… Lab protocols, standard operating procedures…
  10. 10. International Mouse Strain Resource (IMSR) Bramhall et al QUALITY OF METHODS REPORTING IN ANIMAL MODELS OF COLITIS Inflammatory Bowel Diseases, , 2015, “Only one of the 58 papers reported all essential criteria on our checklist. Animal age, gender, housing conditions and mortality/morbidity were all poorly reported…..” The Materials
  11. 11. Turning FAIR into reality Final report and action plan from the European Commission expert group on FAIR data , Nov 2018 The Materials
  12. 12. The Methods Method Reproducibility the provision of enough detail about study procedures and data so the same procedures could, in theory or in actuality, be exactly repeated. Result Reproducibility the same results from the conduct of an independent study whose procedures are as closely matched to the original experiment as possible Procedure = Software, SOP, Lab Protocol, Workflow, Script. Tools, Technologies, Techniques. A whole bunch of them together. Goodman, et al ScienceTranslational Medicine 8 (341) 2016
  13. 13. The Methods Computational Workflows/Scripts Experimental Standard Operating Procedures
  14. 14. Assemble Methods, Materials Experiment Observe Simulate Analyse Results Publish/ Share Results Manage Results Plan Run “I can’t immediately reproduce the research in my own laboratory. It took an estimated 280 hours for an average user to approximately reproduce the paper. Garijo et al. 2013 Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome PLOS ONE.
  15. 15. re-compute replicate rerun repeat re-examine repurpose recreate reuse restore reconstruct review regenerate revise recycle redo robustness tolerance verify compliance validate assurance remix conceptually replicate “show A is true by doing B rather than doing A again” verify but not falsify [Yong, Nature 485, 2012] The R* Brouhaha repair
  16. 16. The R* Nautilus with thanks to Nicola Ferro for the visualisation Repeat Replicate Reproduce Reuse / Generalise
  17. 17. The R* Nautilus with thanks to Nicola Ferro for the visualisation Repeat Same data, set up Same task/goal Same materials Same methods Same group/lab My Research Environment robust, defensible, productive “Micro” Reproducibility
  18. 18. The R* Nautilus with thanks to Nicola Ferro for the visualisation Repeat Same data, set up Same task/goal Same materials Same methods Same group/lab Replicate Same data, set up Same task/goal Same materials Same methods Different group Our Research Environment review, validate, certify Publication Environment review, validate, certify “Sameness” Accountability Trust
  19. 19. The R* Nautilus with thanks to Nicola Ferro for the visualisation Repeat Same data, set up Same task/goal Same materials Same methods Same group/lab Replicate Same data, set up Same task/goal Same materials Same methods Different group Reproduce Different data, set up Same task/goal Same/different materials Same/different methods Different group Their Research Environment review, compare, verify “Similar” Accountability Trust “Macro” Reproducibility
  20. 20. The R* Nautilus with thanks to Nicola Ferro for the visualisation Repeat Same data, set up Same task/goal Same materials Same methods Same group/lab Replicate Same data, set up Same task/goal Same materials Same methods Different group/lab Reproduce Different data, set up Same task/goal Same/different materials Same/different methods Different group/lab Reuse / Generalise Different data, set up Different task/goal Same/different materials Same/different methods Different group/lab Transferred Repurposed Trusted Productivity
  21. 21. The R* Nautilus with thanks to Nicola Ferro for the visualisation Reused Experimental outputs Outputs retained Outputs Used and Shared Outputs Published Not all outputs are worth the burden of metadata unless its automagical and a side-effect
  22. 22. Why does this matter? Moving between different environments Recreating / accessing common environments Fragmented, decentralised, multi-various and complicated … Research Infrastructure Services Assemble Methods, Materials Experiment ObserveSimulate Analyse Results Quality Assessment Track and Credit Disseminate Deposit & Licence Publishing Services Share Results Manage Results Science 2.0 Repositories: Time for a Change in Scholarly Communication Assante, Candela, Castelli, Manghi, Pagano, D-Lib 2015
  23. 23. Why does this matter? Accuracy, Sameness, Change, Dependencies What has been fixed, must be fixed, what variations are valid. We snapshot publications but science does not stay still. Replication may be harder than reproducing and will decay as the tools, methods, software, data … move on or are inherently unavailable. What are the dependencies. What are the black box steps. Results may vary
  24. 24. Why does this matter? More than just “FAIR” data Open Access to data, software and platforms Rich descriptions of data, software, methods • Transparent record of steps, dependencies, provenance. • Reporting robustness of methods, versions, parameters, variation sensitivities • Portability and preservation of the software and the data Should be embedded in Research Practice not a burdensome after thought at publication. Keeping track a side effect of using research tools.
  25. 25. Transparency https://cos.io/our-services/top-guidelines/
  26. 26. Extreme example Precision medicine HTS pipelines Alterovitz, Dean, Goble, Crusoe, Soiland-Reyes et al Enabling Precision Medicine via standard communication of NGS provenance, analysis, and results, biorxiv.org, 2017, https://doi.org/10.1101/191783 parameters
  27. 27. Why does this matter? • Reproducibility is a spectrum • Strength and difficulty depends on context and purpose in the scholarly workflow • Beware reproducibility (and FAIR) dogmatists.
  28. 28. Why does this matter? forced fragmentation and decentralisation distributed knowledge infrastructures De-contextualised Static, Fragmented Lost Semantic linking Contextualised Active, Unified Semantic linking Buried in a PDF figure Reading and Writing Scattered….
  29. 29. Trend: Research Commons & Hubs DOI: 10.15490/seek.1.investigation.56 Snapshot preservation http://fairdomhub.org
  30. 30. Trend: Research Objects context, data, methods, models, provenance bundled together Handling and embracing decentralisation and enabling portability
  31. 31. Trend: Tool/Environment Proliferation built in reproducibility by side effect, reproducibility ramps, disguised as productivity. If only they worked together… Standards and templates for reporting methods, provenance, tracking Tools and platforms for capturing, tracking, structuring, organising assets throughout the whole project research cycle. Shared Cloud-based analysis systems & collaboratories Workflow/Script Automation Containers for executable software dependencies & portability Electronic Lab note books Open source software repositories Models and methods archives Research Commons
  32. 32. Trend: Publication Tool Proliferation mostly as an additional step eLife Reproducible Document Stack publish computationally reproducible research articles online. Data2Paper
  33. 33. Challenges
  34. 34. Provocation: why are we still publishing articles? For Reproducible Research Release Research Objects Jennifer Schopf,Treating Data Like Software: ACase for ProductionQuality Data, JCDL 2012 Analogous to software products and practices rather than data or articles or library practices… Treat ALL Products and ALL Research Like Software Time Higher Education Supplement, 14 May 2015
  35. 35. Acknowledgements • Dagstuhl Seminar 16041 , January 2016 – http://www.dagstuhl.de/en/program/calendar/semhp/?semnr=16041 • ATI Symposium Reproducibility, Sustainability and Preservation , April 2016 – https://turing.ac.uk/events/reproducibility-sustainability-and-preservation/ – https://osf.io/bcef5/files/ • Nicola Ferro • CTitus Brown • Juliana Freire • David De Roure • Stian Soiland-Reyes • Barend Mons • Tim Clark • Daniel Garijo • Norman Morrison • Matt Spritzer • Scott Edmunds • Paolo Manghi …
  36. 36. • Reproducibility rubric https://osf.io/zjvh2/

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