Welcome to ES 2!

Quick links: Campuswire — Provide — JupyterLab — Textbook online — Canvas

This is the home page for ES 2-06, taught by Steven Bell and Joel Grodstein.

Schedule and links

All dates/times are US Eastern time. Note that we’ll switch to daylight savings time on March 14.

General due dates, unless otherwise specified:

Quizzes are due on Fridays at 11:59pm, via the Jupyter notebook.
Labs are due on Sundays at 11:59pm, via provide.

Some links are dead at the moment; they will be filled in as the course gets underway.

Week 1 (Feb 1): Simple calculations

Readings / videos

Think Python, Chapter 1 (The Way of the Program)

Think Python, Chapter 2 (Variables, expressions, and statements)

A visual demonstration of variables (3:46)

Introduction to variables (7:13)

Why use variables? (6:30)

Strings and comments (6:27)

Expressions (4:48)

Printing and indentation (5:18)

Slides from the videos

Friday-quiz #1 (variables & printing, due 2/7). Info on Campuswire

Recitation

Nothing to read this week, just show up!

Lab

Lab 1 — How accurate is testing?

Submit here (due 2/14)

Solution code and questions

Week 2 (Feb 8): Loops, vectors, and plots

Readings / videos

Think Python, Section 4.2 (Repetition)

Think Python, Chapter 7 (Iteration)

Introduction to loops (3:00)

Examples of loops (5:52)

While and nested loops (6:59)

Slides from the videos

Pyplot tutorial (Work through the first 4 plots on this page; we’ll cover the rest later in the course.)

Friday-quiz #2 (loops, due 2/13); follow the same instructions as for quiz #1, but now use quiz2.ipnb

Recitation

Complete these readings and videos before your recitation section, so we can discuss them together.

Calling Bullshit, Chapter 9 (Link on Canvas)

The Laws of Medicine (Link on Canvas)

Discussion questions

Lab

Introduction to simulating infection (5:30)

Basic modeling (10:27)

Individual models (7:46)

Population models (5:26)

herd immunity (5:02)

Slides from the videos

Lab 2 — Simulating disease spread and solutions

Submit here (due 2/21)

Thonny

Thonny is a Python “Integrated Development Environment” (IDE) which lets you write and execute Python code on your computer. It has a number of nice features designed to help you learn Python and programming more generally.

Quick guide to installing Thonny (Python IDE)

Introduction to Thonny (6:25)

Loops in Thonny (5:28)

Adding numpy to Thonny (3:22)

Thonny run to cursor (5:01)

Thonny object inspector (4:06)

You’ll also want to add matplotlib the same way as numpy.

Week 3 (Feb 15): Conditional expressions and functions

No class on Monday (Presidents’ day), Tuesday is a Monday schedule.
Tuesday recitations can either attend at their normal day/time if that works, or pick a different section and let us know (we’ll give you the Zoom link)

Readings / videos

Think Python, Chapter 3 (Functions)

Think Python, Chapter 5 (Conditionals)

Think Python, Chapter 6 (Fruitful functions)

Introduction to functions (6:18)

what functions do (4:46)

functions v2 (6:23)

functions v2 (3:45)

functions v2 (7:07)

functions and scope (6:56)

Slides from the videos

Friday-quiz #3 (functions, due 2/19)… the usual drill

Recitation

Discussion questions on lab #2

Week 4 (Feb 22): Data structures and JSON

Readings

Think Python, Chapter 10 (Lists)

Think Python, Chapter 11 (Dictionaries)

Friday-quiz #4 (data structures, due 2/26)… the usual drill

Recitation

Lab

Lab 3 — Analyzing Tufts CV statistics

Number formatting examples

Submit here (due 3/7).

Week 5 (Mar 1): Tabular data and more plotting

Readings

Think Python, Chapter 8 (Strings)

Think Python, Chapter 14.1-2, 14.4-5 (Files)

Friday-quiz #5 (csv format, regex; due 3/5)

Recitation

Lab

Lab 4 — Interpreting NY Times CV statistics; nominally due 3/14

Week 6 (Mar 8): Curve fitting and correlation

Readings / videos

What good are arrays? (4:57)

Egg carton demo (3:59)

Intro to Numpy arrays (5:55)

Array operations (6:55)

Array slices(10:56)

Array issues, part 1 (7:41)

Array issues, part 2 (6:06)

Array wrapup (10:59)

Slides from the videos

Recitation

Lab

Lab 5 — When will we get vaccinated?; nominally due 3/21 here

Week 7 (Mar 15): Summary statistics, histograms

Readings

Curve fitting in the news

Calling Bullshit chapter 4 – correlations. Access it directly or through your Canvas Reading List (we only need through page 56).

No Friday-quiz this week

Recitation

Play with curve fitting, discuss the “curve fitting in the news” article.

Lab

Lab 6 — Histograms; nominally due 3/28 here

Week 8 (Mar 22): Histograms

Readings

Some nice reading on histograms?

Recitation

talk about histograms and about correlation/causation

Week 9 (Mar 29): Sampling errors

Readings

Calling Bullshit chapter 6 – sampling errors (especially hot vs. nice). Access it directly or through your Canvas Reading List.

Review the array-wrapup (10:59) slides on advanced indexing if you like

Computing correlation coefficients with Numpy, taken from the admissions lab.

Recitation

talk about sampling errors (roughly CB chapter 6 up through hot vs. nice), Numpy advanced indexing and correlation coefficients

Lab

Lab 7 — Tufts admissions; nominally due 4/11 here

Survey

Here’s a survey about your general attitudes towards engineering. The combination of this and the end-of-semester post-survey are worth 1 point.

Week 10 (Apr 5): Random trials and P values

Readings

Calling Bullshit chapter 6 – sampling errors (especially musicians and early death). Access it directly or through your Canvas Reading List.

A Covid-related version of survivor’s bias: on Canvas or medscape

Numpy.random.random(), taken from the hospital_sim1 lab.

Recitation

more about sampling errors (roughly the rest of CB chapter 6)

Lab

Lab 8 — Hospital sim #1; nominally due 4/18 here

Week 11 (Apr 12): P hacking

Readings

Calling Bullshit chapter 9 – P hacking (we already read the Prosecutor’s Fallacy part).

P values and T tests, taken from the hospital_sim2 lab.

An xckd cartoon about P hacking.

Recitation

P values and P hacking discussion

Lab

Lab 9 — Hospital sim #2; nominally due 4/25 here

Week 12 (Apr 19): What is a virus?

No class on Monday (Patriots’ day), Monday recitations will slip a week.

Readings

Cells

intro (1-4): 3:30

assembly (5-8): 9:33

dogma1 (9-13): 7:26

dogma2 (14-19): 11:17

Viruses

viruses (1-6); 10:03

immun1 (7-13); 10:16

immun2 (14-19); 9:35

Recitation

Viruses and your immune system

Week 13 (Apr 26): Understanding vaccines

Readings

Vaccines

history (1-5); 6:55

traditional (6-9); 6:35

DNA (10-14); 8:36

RNA (15-18); 8:58

Recitation

Week 14 (May 3): Wrapping up!

Classes end Wednesday; only Monday recitations will meet this week.