Scientific Open Source Software: meat and bits but not papers. Is it real work?

A discussion on the role of open source software in science, its sustainability and current outlook.

Co-authored with Lindsey Heagy (https://lindseyjh.ca).

Video of the presentation available at: https://cdac.uchicago.edu/insights/fernando-perez-scientific-open-source-software

1. Fernando Pérez Lindsey Heagy Scientific Open Source Software: meat and bits but not papers. Is it real work?
2. A really odd career Physics PhD: Lattice QCD Simulations Applied Math Postdoc: numerical algorithms
3. A really odd career Physics PhD: Lattice QCD Simulations Applied Math Postdoc: numerical algorithms
5. –Hamming'62 “The purpose of computing is insight, not numbers”
6. Maslov’s hierarchy of OSS Services and content Software Standards and Protocols Community
7. Services/Software
8. 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 …
9. Standards and Protocols
10. Core ideas of the web: HTTP & HTML HTML: format to represent content HyperText Markup Language HTTP: protocol to connect clients and servers HyperText Transport Protocol Image credit: eviltester.com
11. Core ideas of Jupyter Document Format https://github.com/CamDavidsonPilon/Probabilistic-Programming-and-Bayesian-Methods- for-Hackers Interactive Computing Protocol SUB SUB DEAL Client SUB DEAL DEAL DEAL ROUT PUB ROUT ROUT Kernel ØMQ + JSON
12. A language agnostic protocol
13. A language agnostic protocol u a l j i
14. A language agnostic protocol u a l j i
15. A language agnostic protocol u a l j i ~100 different kernels: https://github.com/jupyter/jupyter/wiki/Jupyter-kernels
16. Community
17. IPython: an afternoon hack, 2001
18. Plus ~ 1500 more Open source contributors! A true team effort
19. Formalized governance Formal fiscal sponsorship Brian Granger Cal Poly, Amazon Me :)
20. Educational impact: a view from Berkeley
21. Fall 2018 Data 100: ~800 students Data 8: ~1,300 students
22. With these tools, we provide: ❖ Broad disciplinary reach and impact of statistical thinking. ❖ Drastically lowered barriers to student access - intellectual and economic. ❖ Lowered barriers for faculty* to engage with statistical and computational ideas. ❖ (*) typically from non computational/statistical domains) Organizational and intellectual leadership: Cathryn Carson, Ani Adhikari, John DeNero, … (many more)
23. Not just teaching toys: real research tools
24. Reproducible Research 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, WaveLab and Reproducible Research, 1995
25. mybinder.org: shareable reproducibility github.com/freeman-lab Explicit Dependencies + + Origins: Jeremy Freeman’s lab at Janelia farm. That “incentives" business…
26. LIGO: September 14, 2015
27. The song of the universe http://bit.ly/black-holes-woop
28. The song of the universe http://bit.ly/black-holes-woop
30. April 18/19, 2019: Shep Doeleman & Katie Bouman
31. Geosciences: research & education Lindsey Heagy, Berkeley 2019 GWH Career Achievement Award for outstanding junior scientist SimPEG: https://simpeg.xyz http://geosci.xyz
32. Pangeo: open geosciences (and more!) Harnessing the power of cloud computing to study the whole earth interactively. https://pangeo.io Ryan Abernathey Joe Hamman
33. Pangeo: open geosciences (and more!) Harnessing the power of cloud computing to study the whole earth interactively. https://pangeo.io Ryan Abernathey Joe Hamman
34. Pangeo: open geosciences (and more!) Harnessing the power of cloud computing to study the whole earth interactively. https://pangeo.io Ryan Abernathey Joe Hamman
35. Jupyter meets the Earth: newly funded NSF grant - $2M/3y • CMIP6 Climate data analysis • Large scale hydrological modelling • Geophysical simulations and inversions • Data discovery through JupyterLab • Interactivity: Widgets & Dashboards • JupyterHub: Using and managing shared computational infrastructure Fernando Perez Joe Hamman Laurel Larsen Kevin Paul Lindsey Heagy Chris Holdgraf Yuvi Panda Research use-cases Tech developments
37. Jupyter - funding and resources
38. So you want to build Data Science tools in academia…
39. Career paths?
40. John Hunter Pediatric Neurology
41. John Hunter
43. Scientific Open Source: Despite (direct) federal $$ support ❖ “Indirectly”, lots of $ have supported Scientific OSS projects/tools. ❖ Under the cover of domain-focused work.
44. Traditional software infrastructure funding Yes, it’s true, the budget is gone again… But you can’t deny that now, we get here in an instant! Quino (Argentinian cartoonist)
45. Contrasts in culture and incentives Open Source Academia Credit Distributed PI & hierarchy Output/artifacts Continuous & Project-specific Discrete papers Collaborators Fluid: professionals, volunteers, … Structured, funding-dependent Governance/ decision making Open, community based Top-down, PI Authorship Fluid, roles can evolve, no clear “first/ senior” author Need to say more? Peer review Continuous, open, pervasive, friendly The opposite Value metric Utility, need, impact “Novel and transformative”
46. “The Stack”: a complete ecosystem
47. “The Stack”: a complete ecosystem
48. “The Stack”: a complete ecosystem Domain-agnostic backbone/trunk
49. “The Stack”: a complete ecosystem Domain-agnostic backbone/trunk • Not “real CS” • Not “real research” • Nobody’s problem • Yet critical to everybody else
50. Organizations that fill current gaps
51. Skills in education The Carpentries Tracy Teal Executive Director
52. Skills in education The Carpentries Tracy Teal Executive Director The Society of Research Software Engineering was founded on the belief that a world which relies on software must recognise the people who develop it. https://society-rse.org The Society of Research Software Engineering Career paths
53. Open communities & industry Leah Silen Executive Director Andy Terrel President
54. leadership, management, organization building
55. JOSS/JOSE: academic publication credit Arfon Smith STScI, Baltimore Lorena Barba GWU
56. HackWeeks: training and hacking meet domain research Training?
 From undergrads to senior PIs In the same room!!
57. HackWeeks: training and hacking meet domain research Training?
 From undergrads to senior PIs In the same room!!
58. HackWeeks: training and hacking meet domain research Training?
 From undergrads to senior PIs In the same room!!
59. HackWeeks: training and hacking meet domain research Training?
 From undergrads to senior PIs In the same room!!
60. HackWeeks: training and hacking meet domain research Training?
 From undergrads to senior PIs In the same room!!
61. HackWeeks - a reproducible model https://doi.org/10.1073/pnas.1717196115 Daniela Huppenkothen http://huppenkothen.org/
62. An economic and organizational problem
63. Catastrophic Success: an economic problem (2015 data) https://arxiv.org/abs/1507.03989
64. Catastrophic Success: an economic problem (2015 data) https://arxiv.org/abs/1507.03989 ❖ MathWorks: 4,000+ employees ❖ Wolfram: 800 employees ❖ IDL/Harris: 17,000 employees
65. Investing to hedge strategic risks ❖ It takes investment to have a seat at the table. ❖ Scientists (and their funders) want a voice? ❖ The code is already out - whose voices will shape it?
66. Bang for the buck? ❖ Federal 2018 R&D budget: $176.8B (AAAS analysis) ❖ What fraction of R&D today depends critically on computing? 10%? 30%? 50%? ❖ $200M is ~0.1% of that. ❖ $200M annually (well spent) would have major impact.
67. “Well spent” That should be easy… ❖ Some features of successful, resilient projects ❖ Broad community engagement ❖ Actively managed pipeline for new contributions ❖ Capacity for short and long-term planning ❖ Writing code only small part of the job ❖ Treat OSS projects like real, complex organizations
68. It’s in the air… "many projects of immense infrastructural importance are simultaneously fundamental to multiple business models and also chronically underfunded”
69. Ford Foundation report, authored by Nadia Eghbal @nayafia
70. Multi-stakeholder governance @nayafia
71. ❖ Economic incentives and sustainability ❖ Governance models ❖ Roles and professional career paths ❖ Multi-stakeholder organizational structures OSS is a lot more than software
72. Thank you (Bay Area team) Current (Berkeley, LBNL, Bloomberg) Stacey Dorton, Lindsey Heagy, Chris Holdgraf, Yuvi Panda, Ryan Lovett, Shreyas Cholia, Shane Canon, Rollin Thomas, Jason Grout Former Berkeley Min Ragan-Kelley, Paul Ivanov, Thomas Kluyver, M Pacer, Matthias Bussonnier, Jessica Hamrick, Ian Rose, Jamie Whitacre.
73. In Memoriam - John Hunter, 1968-2012