reproducibility as the engine of science: tools for reproducible research

Presented at the workshop: "Scientific publication beyond the text: Sharing research objects"

https://library.stanford.edu/events/scientific-publication-beyond-text-sharing-research-objects

Thanks to Rowan Cockett, Chris Holdgraf and Fernando Perez for helping shape these ideas and this presentation.

Transcript

1. reproducibility as the engine of science: tools for reproducible research Lindsey Heagy UC Berkeley @lindsey_jh
2. hello (a bit about me) geophysical inversions open-source software open research & education geoscience + data science +
3. questions in the geosciences Observations / Data After Hamman, 2018 Theory & Ideas EMAG2: Earth Magnetic Anomaly Grid (2-arc-minute resolution). Image credit: Dom Fournier (toolkit.geosci.xyz) Simulations, Computation
4. what are the ingredients? • questions • domain knowledge • software • data • infrastructure
5. evolving research outputs & audiences Variety of “consumers”: • peers • students • decision makers & the public Drives diversity in outputs • journal publications • web apps • educational resources • ...
6. on reproducibility start here on extensibility “publish” contribution
7. tools and platforms for researchers
8. scientific software *Python ecosystem
9. interactive, exploratory computing a community of people and an ecosystem of open tools and standards for interactive computing
10. Jupyter notebooks
11. using notebooks
12. JupyterLab: a grand unified theory of Jupyter Huge Team Effort! C. Colbert, S. Corlay, A. Darian, B. Granger, J. Grout, P. Ivanov, I. Rose, S. Silvester, C. Willing, J. Zosa-Forde …
13. JupyterLab and notebooks ++
14. JupyterLab: more than notebooks
15. JupyterLab: data
16. JupyterLab is extensible: FlyBrainLab An Interactive Computing Platform for the Fly Brain BIONET Group, Columbia University http://www.bionet.ee.columbia.edu Aurel A. Lazar (PI) Tingkai Liu Mehmet K. Turkcan Chung-Heng Yeh Yiyin Zhou http://fruitflybrain.org
18. notebooks on a or HPC jupyter.org/hub host pre-configured environments on shared infrastructure
19. JupyterHub
20. myhub.org fancy machine in the cloud
21. myhub.org
22. myhub.org environments
23. myhub.org interfaces environments
24. AUTHENTICATION myhub.org interfaces environments
25. JupyterHub distributions The Littlest JupyterHub tljh.jupyter.org JupyterHub on Kubernetes z2jh.jupyter.org A pre-configured JupyterHub setup with sensible defaults and lots of documentation, fit for many use-cases ☁
26. Scalable in both users and in resources Uses Docker for environment management Agnostic to the provider and hardware configuration Zero to JupyterHub for Kubernetes z2jh.jupyter.org
27. Data 8 at UC Berkeley ~2800 students (Spring/Fall 2019)
28. tools and platforms for researchers
29. National infrastructure from K-12 to HPC J. Colliander, I. Allison, B. Carra
30. Harnessing the power of cloud computing to study the whole Earth interactively Interactivity Distributed computing Data models / numerics
31. Pangeo architecture
32. Jupyter meets the Earth: an NSF grant (2M / 3Y)! Fernando Pérez Joe Hamman Laurel Larsen Kevin Paul Lindsey Heagy Chris Holdgraf Yuvi Panda Research use-cases Tech developments • Climate data analysis • Hydrology • Geophysics • Data discovery • Interactivity • Cloud/HPC infrastructure For more: http://bit.ly/jupytearth
33. Publication (sharing research with other people)
34. the science more than the paper An article about computational science in a scientific publication is not the scholarship itself, it is merely advertising of the scholarship. The actual scholarship is the complete software development environment and the complete set of instructions which generated the figures. -- Buckheit and Donoho (paraphrasing Claerbout) WaveLab and Reproducible Research, 1995
35. An article about computational science in a scientific publication is not the scholarship itself, it is merely advertising of the scholarship. The actual scholarship is the complete software development environment and the complete set of instructions which generated the figures. (and a place to run the code?) the science more than the paper -- Buckheit and Donoho (paraphrasing Claerbout) WaveLab and Reproducible Research, 1995
36. mybinder.org shareable, interactive, reproducible environments from your public git repository
37. binder binder repo2docker JupyterHub
38. http://bit.ly/black-holes-woop Black holes! LIGO, Sept 14, 2015
39. JupyterBook: computation + context publish a collection of notebooks as an online textbook inferentialthinking.com
40. New development: publishing executable books QuantEcon IAB Jupyter Book PDF HTML ... execution and text content sync citations, cross-refs, rich metadata
41. reaching new audiences
42. on reproducibility start here on extensibility “publish” contribution
43. Reaching new audiences: educational resources
44. Reaching new audiences: educational resources
45. a medium for conversation
46. GeoSci.xyz https://geosci.xyz EOSC 350 26 locations worldwide
47. Groundwater in Myanmar • Bring DC resistivity equipment to Mon state • Train local stakeholders • Provide open-source software and educational resources
48. Reaching new audiences Diverse research outputs: • Papers • Notebooks • Apps • Web-based textbooks “Consumers” of science • Scientists • Students • Public
49. Revisiting “publishing”
50. pdf model capture research in a pdf, peer review, accepted(!) scientist consumers
51. pdf model extending or building on ideas? scientist scientist?
52. pdf model extending or building on ideas? scientist scientist consumers
53. Blurring the line between scientists and audience? • Open tools are ◦ accessible ◦ explorable ◦ extensible
54. An open ecosystem supports the engine of science • Open tools are a starting point for… ◦ reproducibility of work ◦ collaboration at the level of computation ◦ extension of ideas • And provide a trajectory for “consumers” to become creators
55. Thank you! @lheagy lheagy@berkeley.edu @lindsey_jh Special Thanks: Rowan Cockett Chris Holdgraf Fernando Pérez