Week 12 (November 8 – November 14)

Thursday, November 11 (6:00 P.M. – 8:00 P.M., Zoom) Class Session 12
Topics	Review solutions to prior week's coding assignments Jupyter Notebooks
Required Readings	Driscoll, M. (n.d.) Jupyter Notebook: An Introduction. Real Python. Rule A, Birmingham A, Zuniga C, Altintas I, Huang S-C, Knight R, et al. (2019) Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks. PLoS Comput Biol 15(7): e1007007.
Required Recordings	LinkedIn Learning Course -- Python Tools: Jupyter vs PyCharm This short video course provides a quick orientation that will help you understand the relationship between PyCharm and Jupyter. Be aware that it does discuss some features that we do not cover in our introductory course: debugger, version control, and profiling. These are short sections that are probably worth listening to anyway.
Other Resources	Cone, M. (2021). The Markdown Guide Grus, J. (2018). I don't like notebooks. Presentation at O'Reilly JupyterCon. YouTube.

Sunday, November 14 (10:00 A.M. – 11:00 A.M., Zoom) Optional Session
Lab Session	On Sunday mornings from 10:00 AM till 11:00 AM, I will be holding an optional Lab Session using Zoom. Please drop by to ask a question, to discuss solutions to previous assignments, to get help with the current assignment, to discuss the final project, or just to say hello. Please use a headset while participating.

Sunday, November 14, @ 11:55 P.M. Weekly Assignments Deadline
Computing Setup	Create an Anaconda virtual environment for the Jupyter Notebook Assignment Description: In order to do the Jupyter Notebook Assignment, you will need to create an Anaconda virtual environment that includes both Python and the Jupyter packages. To do that, follow the tutorial video below that matches your operating system. Conda 4.6 Cheat Sheet Tutorial Video: Create Anaconda Virtual Environment for the Jupyter Notebook Assignment (Windows) Tutorial Video: Create Anaconda Virtual Environment for the Jupyter Notebook Assignment (macOS) Create Your First PyCharm Project That Includes a Jupyter Notebook Description: Follow this tutorial to create your first PyCharm project that includes a Jupyter Notebook. There is just one version of this tutorial that addresses both Windows and macOS. Tutorial Video: Create Your First PyCharm Project That Includes a Jupyter Notebook
Coding Assignments Due	Jupyter Notebook Assignment Description: Please see the Instructions document below for assignment details. Submit to: Jupyter Notebook Assignment Instructions for Jupyter Notebook Assignment Starter files for Jupyter Notebook Assignment Tutorial Video: Jupyter Notebook Assignment - Part 1 Tutorial Video: Jupyter Notebook Assignment - Part 2 Tutorial Video: Jupyter Notebook Assignment - Part 3 Grading Rubric for Jupyter Notebook Assignment

Sunday, November 14, @ 11:55 P.M.
Weekly Assignments Deadline

Computing Setup

Create an Anaconda virtual environment for the Jupyter Notebook Assignment
Description: In order to do the Jupyter Notebook Assignment, you will need to create an Anaconda virtual environment that includes both Python and the Jupyter packages. To do that, follow the tutorial video below that matches your operating system.
Create Your First PyCharm Project That Includes a Jupyter Notebook
Description: Follow this tutorial to create your first PyCharm project that includes a Jupyter Notebook. There is just one version of this tutorial that addresses both Windows and macOS.
- Tutorial Video: Create Your First PyCharm Project That Includes a Jupyter Notebook

Coding Assignments Due

Jupyter Notebook Assignment
Description: Please see the Instructions document below for assignment details.
Submit to: Jupyter Notebook Assignment

Weekly Course Schedule – Fall 2021