Prof. Pérez and GSI Sapienza , Department of Statistics, UC Berkeley
Below is our current plan for the course. This is not a contract: it is a plan, and it may change substantially as the semester unfolds, especially given extra uncertainties due to COVID-19.
The table of contents on the left pane has links to lectures and labs. The following are live executable links that use the nbgitpuller service to give you a current copy from git of the given content, ready to be run in the Spring 2022 Berkeley hub. You can use these links in order to run the content conveniently without manual git work.
Note that all lecture videos are posted on the bCourses "Lectures" playlist for the course (this link is accessible only to Berkeley personnel).
- Jan 19. Logistics and intro to Git.
- Jan 26. JupyterHub, JupyterLab and its various tools, dotfiles for reproducible personal configuration.
- Feb 2. Github, Git tutorial continued. (Note: this lecture has damaged audio for the 2nd half).
- Feb 9. Git visuals, an overview of Project Jupyter. IPython - beyond plain Python.
- Feb 16. Rich output in Jupyter, VNC and virtual desktops in JupyterLab. Introduction to nbdime.
- Feb 23. Climate data, xarray and open science at NASA. Guest lecture by Dr. Chelle Gentemann.
- March 2. Merge conflicts with nbdime (sample repo). Custom display logic in Jupyter. (Note: this lecture has damaged audio for the last ~ 45 minutes).
- March 9. Automation and Make, based on the Carpentries' tutorial.
When an assignment consists of multiple articles, you should submit a summary paragraph and idea highlight paragraph per each separate article.
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#1, due Jan 31, 2022: Developing open source scientific practice.
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#2, due Feb 14, 2022: Keith Baggerly and the Potti & Nevins Cancer Scandal. These are actually two videos, not reading, but the same format applies (short summary, then idea highlight; in this case only one paragraph of eacy kind is to be submitted, as the 60 minutes video is a short overview meant to give you context, while the talk contains more dense ideas):
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#3, due Feb 22: Earth and Climate Science in the Cloud
- Perspectives on Data Reproducibility and Replicability in Paleoclimate and Climate Science.
- Gentemann et al. 2021, Science Storms the Cloud.
- Gentemann et al. "Satellite sea surface temperatures along the West Coast of the United States during the 2014–2016 northeast Pacific marine heat wave.". For this paper, start thinking about reproducibility issues with it. The lead author, Dr. Chelle Gentemann, will be our guest lecturer on Feb 23, and she will discuss aspects of this work. Later we will follow up with a reproducibility attempt around this paper.
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#4, due Feb 28: Core concepts
- Barba 2018, Terminologies for Reproducible Research
- Reproducibility and Replicability in Science, chapter 2 (SCIENTIFIC METHODS AND KNOWLEDGE).
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#5, due Mar 7: Foundational classics
- Schwab, M., Karrenbach, N., Claerbout, J. (2000) Making scientific computations reproducible, Comp. Sci. Eng. 2(6):61–67, doi: 10.1109/5992.881708.
- Reproducible Research, by the Yale Law School Roundtable on Data and Code Sharing, Comp. Sci. Eng. 12(5): 8–13 (Sept.-Oct. 2010), doi:10.1109/mcse.2010.113.
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#6, due Mar 14: Jupyter in Computational Research
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No assignment Mar 21, Spring Recess.
NOTE: the selections below are still subject to change
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#7, due Mar 28: Computational challenges
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#8, due Apr 4: Open Source Software and Open Science - these are four easy "ten simple rules for...":
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#9, due Apr 11: Computational challenges
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#10, due Apr 18: Open Source and Open Science
- Open Source Software Policy Options for NASA Earth and Space Sciences, 2018. Chapter 4, Lessons Learned from Community Perspectives.
- Open Science by Design, Realizing a Vision for 21st Century Research (2018). Chapter 4, A VISION FOR OPEN SCIENCE BY DESIGN.
- Turk 2013, How to Scale a Code in the Human Dimension
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#11, due Apr 25: Earth and Climate Science in the Cloud
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No assignment May 2, RRR Weeek, but if you'd like some fun reading for intellectual inspiraiton, I recommend Ten Simple Rules for Doing Your Best Research, According to Hamming.
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#12, due May 9: Earth and climate science