**Time**: 11:15 - 12:05 MWF, January 7th to April 26th, 2018**Location**: Osmond Room 201**Special Computer labs**: January 9th and 11th, Sparks 15 Mac lab**Office hours**will be Mondays, 3:30 - 4:30, or by appointment.**Textbooks**:- Online Notes for a textbook, including data sets and code examples. These are still under construction. Feel free to offer feedback when you see mistakes, or confusing text.
- Signal and the Noise by Nate Silver (founder of Five Thirty Eight) will be used to discuss the nature of modelling in the large.
- A suggested textbook for self-help with python coding is A student's guide to python for physical modeling by Kinder and Nelson. It is a very new and nice book. If you have other suggestions, let me know.
- Overleaf is an online implementation of LaTex that you may find useful for writting up your homework. LaTex is free, so you can get and install it ourself and preserve your rights.

**Software**: For computer programming in python at home, consider Anaconda or Canopy. Both supply graphical user interfaces. Canopy's is built-in. Anaconda uses Spyder

- Monday, January 7th
- Course introduction
- Fermi models
- Homework problems

- Wednesday, January 9th
**Class in Sparks 15a**- Lab 1: Introduction to python

- Friday, January 12th
**Class in Sparks 15a**- Lab 2: Scientific computing with python
- Extra: Using LaTex to write your homework

- Monday, January 14th
- Class back in Osmond 201
- Trigonometry -- triangulation and spherical trig
- Homework problems

- Wednesday, January 16th
- Coordinate geometry covering the trammel and cycloid.
- Homework problems

- Friday, January 18th
- Monday, January 21
- No class, Martin Luther King day

- Wednesday, January 23
- Least squares through the charting example.
- Homework problems

- Friday, January 25
- Power laws and exponentials fit to data using least squares
- Homework problems

- Monday, January 28
- Wednesday, January 30
- Friday, February 1
- Monday, February 4
- Wednesday, February 6
- Linear Compartmental modelling
- Differential equation numerics
- Homework problems
- Read Chapter 1 and 2 of "Signal and the Noise" for Wednesday, Feb. 13th.
- Read the research study by Thibodeau and Boroditsky published in PLoS 1 and the associated newspaper article Metaphors can change our opinions in ways we don't realize by S. Rathje. While reading these articles, keep in mind our own studies this semester, and see if you can find a way to apply it to these readings.

- Friday, February 8
- Monday, February 11
- In-class compartmental modelling group work

- Wednesday, February 13
- Discussion of reading of Chapters 1 and 2 of Silver.

- Friday, February 15
- Modelling discussion of Thibodeau and Boroditsky and the associated article Metaphors can change our opinions in ways we don't realize by S. Rathje.
- Discussion of model fitting
- Compartmental models as metaphors
- Homework problems (see new problems in Homework 4 below)
- Read Chapter 3 of Silver for Wednesday next week

- Monday, February 18
- Review of complex variables
- Mirror equation section of geometric optics

- Wednesday, February 20
- Penn Stat Snow day

- Friday, February 22
- Mechanics and Newton's laws
- Flight using Newton's laws

- Monday, February 25
- Mechanics and Newton's laws
- Flight using Newton's laws

- Wednesday, February 27
- Friday, March 1
- Midterm exam

- Homework 1, due Friday, January 25th Answers
- Homework 2, due Friday, February 1st Answers
- Homework 3, due Friday, February 8th Answers
- Homework 4, Postponed! now due Friday, February 22nd

You will have to do two projects over the course of this class.

*Review report on a published paper*. Reports may be completed alone or with a partner. Find a paper in a peer-reviewed scientific journal. Review the mathematical modelling content of the paper, explaining it in your own words. Reproducing any important figures (or produce your own supplemental figures). Your report should be less than 10 pages.- Due Friday, March 1.
- Topic paper choices due, Friday, February 8th. Finding a good paper can be hard. One strategy is to pick a field or topic and then to trace back through the literature to seminal papers on the topic. Newer papers often have more sophisticated mathematical methods, so older papers will probably be easier to deal with.
- Reports will be graded on the quality and clairity of their review. Correctly identifing and explaining previously un-documented mistakes in a paper would be awesome, but confirming results is good as well.

- Independent modelling project of your choice, with instructor approval.
- Topics due Friday, March 30th
- Due Friday, April 27. Handed in in paper form.
- In your project, you should describe a phenomena or question, construct a mathematical model of this phenomena, and then analyze your model in a way that helps us understand the original phenomena.
- Projects should be 10 pages or less.
- Remember to include a bibliography to any references used.
- If you write code as part of your analysis, include that code as an appendix at the end. This appendix does not count toward the page limit.
- Project ideas

For a Black Mathematician, What It’s Like to Be the ‘Only One’

ASA p-Values statement and a letter in response by Ionides, Giessing, Ritov and Page

A brand new book Lost in Math: How Beauty Leads Physics Astray by Sabine Hossenfelder looks quite good, and reflective of some of my perspective. See my response to Euginia Cheng and Max Tegmark, and David Orrell's book Truth or Beauty: Science and the Quest for Order.

The theory of glass is still an open modelling project! (thanks, Muhammad, for pointing this out)

Cuckoo filters as an improved algorithm for testing set membership.

There is now a tool to convert images of equations to LaTex, though this still probably doesn't handle hand-written equations well.

A new scandal of papers that may have been manipulated to produce attractive but misleading results.

So you want to learn to program in Python and you don’t have a lot of time

Our new pirate queen of science, an expose.

Self-organizing maps suggest good paths for the the Travelling salesman problem

For a formal, structured introduction to computer programming using python, MIT's online course Introduction to Computer Science and Programming is a very helpful reference. Check it out, if you feel like you need more background.

A new textbook on python for scientific computing, A Student's Guide to Python for Physical Modeling, by Kinder and Nelson.

Python coding puzzles aka pytudes.