**Time**: 11:15 - 12:05 MWF, January 8th to April 27th, 2018**Location**: Willard Bldg 351**Special Computer labs**: January 10th and 12th, Huck Life Sciences Bld 004**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.

**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

There will be two exams.

- There will be a midterm on Monday, February 26th, in class.
- There will also be a final exam, Tuesday, May 1, 10:10 am, Willard Bldg 75.

- Monday, January 8th
- Course introduction
- Fermi models

- Wednesday, January 10th
**Class in Huck 004**- Lab 1: Introduction to python

- Friday, January 12th
**Class in Huck 004**- Lab 2: Scientific computing with python

- Wednesday, January 17th
- Friday, January 19th
- Least Squares
- We will skip the lecture on spherical trigonometry for the moment, but feel free to read it and let me know what you think.

- Monday, January 22th
- Wednesday, January 24th
- Friday, January 26th
- Monday, January 29th
- Wednesday, January 31th
- Friday, February 2nd
- continued -- Mass Action, Bean Bags, and Orange Mites

- Monday, February 5th
- Complete pages 1 and 2 of the Compartmental Modelling Practice handout.

- Wednesday, February 7th
- snowday

- Friday, February 9th
- Complete page 4 of the Compartmental Modelling Practice handout.
- Handout on translation rules for the law of mass action between hypergraph representations, reactions, and differential equations.

- Monday, February 12th
- Wednesday, February 14th
- Friday, February 16th
- Monday, February 19th
- Wednesday, February 21st
- Friday, February 23st
- Midterm review and Markov Chain state spaces (if time permits)

- Monday, February 26th
- Midterm exam

- Wednesday, February 28th
- Return Midterms. See Exam 1 comments
- Complete discussion of Markov chain state spaces

- Friday, March 2nd
- Monday, March 12th
- Wednesday, March 14th
- Dimensional analysis continued

- Friday, March 16th
- Monday, March 19th
- Wednesday, March 21st
- Friday, March 23rd

Homework problems will be assigned at the end of each lecture, but also posted here. Assignments will be collected every two weeks.

- Due Wednesday, January 10.
- Due Wednesday, January 24.
- Read Chapters 1 and 2 of Nate Silver's
*The Signal and the Noise* - Homework 1

- Read Chapters 1 and 2 of Nate Silver's
- Due Wednesday, February 7.
- Homework 2 and answers

- Due Friday, February 9.
- Read chapters 3 and 4 of
*The Signal and the Noise*for quiz

- Read chapters 3 and 4 of
- Due Wednesday, February 21.
- Due Friday, March 16.
- Homework 4 (now complete)
- Extra office hours will be held Wednesday afternoon, March 14th.

- Due Wednesday, March 28.
- Homework 5 (incomplete)

- Due Wednesday, April 4.
- TBA

- Due Wednesday, April 18.
- TBA

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 2.
- Topic paper choices due, Friday, February 9th. 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.
- Project ideas

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 donâ€™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.