The practice of reproducible research: case studies and lessons from the data-intensive sciences

Part I. Practicing reproducibility. Assessing reproducibility / Ariel Rokem, Ben Marwick, and Valentina Staneva 
 The Basic reproducible workflow template / Justin Kitzes 
 Case studies in reproducible research / Daniel Turek and Fatma Deniz 
 Lessons learned / Kathryn Huff 
 Building toward a future where reproducible, open science is the norm / Karthik Ram and Ben Marwick --
Part II. High-level case studies. Case Study 1. Processing of airborne laser altimetry data using cloud-based Python and relational database tools / Anthony Arendt, Christian Kienholz, Christopher Larsen, Justin Rich, and Evan Burgess 
 Case Study 2. The trade-off between reproducibility and privacy in the use of social media data to study political behavior / Pablo Barberá 
 Case Study 3. A reproducibe R Notebook using Docker / Carl Boettiger 
 Case Study 4. Estimating the effect of soldier deaths on the military labor supply / Garret Christensen 
 Case Study 5. Turning simulations of Quantum Many-Body Systems into a Provenance-Rich publication / Jan Gukelberger and Matthias Troyer 
 Case Study 6. Validating statistical methods to detect data fabrication / Chris Hartgerink 
 Case Study 7. Feature extraction and data wrangling for predictive models of the brain in Python / Chris Holdgraf 
 Case study 8. Using observational data and numberical modeling to make scientific discoveries in climate science / David Holland and Denise Holland 
 Case Study 9. Analyzing bat distributions in a human-dominated landscape with autonomous acoustic detectors and machine learning models / Justin Kitzes 
 Case Study 10. An analysis of household location choice in major US metropolitan areas using R / Andy Krause and Hossein Esteri 
 Case Study 11. Analyzing cosponsorship data to detect networking patterns in Peruvian legislators / José Manuel Magallanes 
 Case Study 12. Using R and related tools for reproducible research in archaeology / Ben Marwick 
 Case Study 13. Achieving full replication of our own published CFD results, with four different codes / Olivier Mesnard and Lorena A. Barba 
 Case Study 14. Reproducible applied statistics: is tagging of therapist-patient interactions reliable? / K. Jarrod Millman, Kellie Ottoboni, Naomi A.P. Stark, and Philip B. Stark 
 Case Study 15. A dissection of computational methods used in a biogeographic study / K.A.S. Mislan 
 Case Study 16. A statistical analysis of salt and mortality at the level of nations / Kellie Ottoboni 
 Case Study 17. Reproducible workflows for understanding large-scale ecological effects of climate change / Karthik Ram 
 Case Study 18. Reproducibility in human neuroimaging research: a practical example from the analysis of diffusion MRI / Ariel Rokem 
 Case Study 19. Reproducible computational science on high-performance computers: a view from neutron transport / Rachel Slaybaugh 
 Case Study 20. Detection and classification of cervical cells / Daniela Ushizima 
 Case Study 21. Enabling astronomy image: processing with cloud computing using Apache Spark / Zhao Zhang --
Part III. Low-level case studies. Case Study 22. Software for analyzing supernova light curve data for cosmology / Kyle Barbary 
 Case Study 23. pyMooney: generating a database of two-tone Mooney images / Fatma Deniz 
 Case Study 24. Problem-specific analysis of molecular dynamics trajectories for biomolecules / Konrad Hinsen 
 Case Study 25. Developing an open, modular simulation framework for nuclear fuel cycle analysis / Kathryn Huff 
 Case Study 26. Producing a journal article on probabilistic tsunami hazard assessment / Randall J. Le Veque 
 Case Study 27. A reproducible neuroimagining workflow using the automated build tool "Make" / Tara Madhyastha, Natalie Koh, and Mary K. Askren 
 Case Study 28. Generation of uniform data products for AmeriFlux and FLUXNET / Gilberto Pastorello 
 Case Study 29. Developing a reproducible workflow for large-scale phenotyping / Russell Poldrack 
 Case Study 30. Developing and testing stochastic filtering methods for tracking objects in videos / Valentina Staneva 
 Case Study 31. Developing testing, and deploying efficient MCMC algorithms for hierarchial models using R / Daniel Turek.