Week 15

Poster Session on Thursday 5/3

• The poster session will be held from 9:15 to 10:45 am in McClelland Park lobby (across the street to the East from Park Student Union). Map: http://map.arizona.edu/.
• Plan to arrive between 8:45 am and 9:00 am to allow time to sign in and set up your poster.

Due on Monday 5/7

• Final report.
• Written end-of-semester reflection: In one to two single-space typed pages, please reflect and describe your work and discoveries on the modeling project this semester. Be sure to include a description of your contributions and also your thoughts on how or whether this activity helped your professional development or influenced your professionalism in team work and collaboration, communication, and problem solving.
• Please note that both D2L folders close at 6:15 pm on 5/7.

Please remember to fill out the online TCEs

• Any feedback you may have on the course content and in-class activities, as well as online notes and assignments will be greatly appreciated.
• Thank you!

Week 14

Poster due on Thursday 4/26

• Please submit PDF and PPTX versions of your poster. The D2L submission folder is called Poster and closes at 2 pm on 4/26.
• The PowerPoint template is set up to have a print size of 36 by 24 inches when saved as a PDF. If you use Google Slides to edit your poster, please make sure that when you export the document in PowerPoint format, the print size has not changed.
• To check the size, save the PowerPoint file as a PDF. Do not use the "Print as PDF" option since this would add blank spaces around the poster to match the letter-size aspect ratio. Then look at the properties of your PDF file. In the Description tab, under Advanced, it should say: Page Size: 36.00 x 24.00 in. If it doesn't, please fix the problem before uploading your poster to the submission folder.
• Don't forget to register your group for the poster session.

Quiz on Thursday 4/26

The quiz will be on one or more of the following problems.

• Problems # 1 and 2 p. 116, # 3, 5, 8, and 9 p. 117, # 12 p. 118.

Week 13

Quiz on Thursday 4/19

The quiz will be on one or more of the following problems.

• Problems # 1, 2 and 4 p. 84, # 5 p. 85.
• Problems # 1 and 2 p. 95; # 3, 4, and 5 p. 95.

For Thursday 4/19

Please bring a draft of your poster to class. A template is available on the D2L course site. Try not to deviate from the general layout if possible. After the quiz, you will work in groups on your poster. I will provide feedback on your current draft and answer any questions you may have on its content and organization.

Week 12

Due Thursday 4/12

Population Dynamics Lab: place your homework, in the form of a single file in PDF format, in the D2L Assignment Submission Folder called Population Dynamics Lab. Please note the folder closes at 2 pm on 4/12.

Week 11

Quiz on Thursday 4/5

To prepare for the quiz, please review the contents of Chapter 5, on single species models. You should be able to do any of the homework problems on pages 69-72.

Week 10

Quiz on Thursday 3/29

The quiz will be on one or more of the following problems.

• Problems # 2 and 4 p. 69, # 5, 6 and 8 p. 70, # 11 and 14 p. 71.

Week 9

Due Thursday 3/22

In-class midterm presentations. Prepare a 15-minute presentation describing your group, your project, and your results so far. Guidelines are below. Groups 1, 3, 4, and 7 will present on 3/22 and Groups 2, 5, 6, and 8 on 3/27.

Before Thursday's class, each group should place a PDF copy of their presentation in the D2L folder called Midterm Presentation. Please note that the folder closes at 2 pm on 3/22.

Guidelines for midterm presentations

• Amend the slides you used for your initial presentation: keep slides 1-4 (see Week 3 assignment below) and replace Slide 5 by a description of your results so far. Make sure to take into account the feedback you received after your first presentation: fix any typos, address issues, fix references, etc. Add slides discussing your results and describing what remains to be done.
• Use as many slides as needed, keeping in mind that pictures and/or videos are useful visual aids, and that your presentation should not exceed 15 minutes.
• If you have developed codes that run reasonably quickly, consider demonstrating how they work during your presentation.
• Also take into account my comments on your midterm report: be prepared to address any questions I raised, make sure to fix any typos or calculation errors, etc. It should be clear from your presentation that you have understood my comments and have thought about how to address them.
• Each team member should contribute to the presentation in a significant way and be able to answer any question.

Week 8

Due Thursday 3/15

Download and read the PDF version of R. May's article entitled Simple mathematical models with very complicated dynamics. As usual, you will need to use your UA credentials to access the file. Then answer questions (1), (3), (5), (6), (7), (12), (13), and (14) of Problem # 15 on page 72 of the class notes, plus two questions of your choice, chosen among the remaining questions.

Please place your homework, in the form of a single file in PDF format, in the D2L Assignment Submission Folder called Homework 2. Please note the folder closes at 2 pm on 3/15.

Week 7

For Tuesday 2/27

Please bring a draft of your report to class. I will answer your questions and provide comments on the overall structure and organization of your draft.

Reports due on Thursday 3/1

Please place your report, in the form of a single file in PDF format, in the D2L Assignment Submission Folder called Midterm Report. Please note the folder closes at 2 pm on 3/1.

Quiz on Thursday 3/1

The quiz will be on one or more of the problems at the end of the section on the nonlinear pendulum, pages 32-39.

Week 6

Start Drafting your Report

• Midterm project reports are due before Spring Break.
• As usual, do not paraphrase, include appropriate references, and credit your sources. If you reproduce figures or tables from the articles you read, explain how they were reproduced/obtained, and reference the original articles in the captions.

Recommended Report Components

1. Abstract: in a few sentences, describe what your project is about, what type of model you are using, what results you have obtained, as well as their significance.
2. Introduction: describe the problem that is being addressed as well as its significance/importance. Use information from the context articles provided as well as from your literature searches.
3. Methods: describe any data collection process, as well as the model you are using. Clearly explain what assumptions are being made and how the model works. For agent-based models, make sure to describe how each agent is expected to behave in each situation it may encounter.
4. Results: for a midterm report, these will probably be preliminary. Illustrate that the components (codes, model equations) already developed as part of the modeling process work as they should. Perform a dimensional analysis of your model and identify relevant scales or dimensionless combinations of parameters.
5. Discussion: summarize what you have accomplished so far as part of the project and discuss your results: what works as expected, what needs to be addressed, what remains to be done.
6. Conclusion: summarize the contents of your report and consider possible extensions of your work.

Quiz on Thursday 2/22

The quiz will be on one or more of the following items.

• Problems # 11 p. 35, # 18, 19, 20 and 21 p. 37, # 22 and 23 p. 38.
• For Problems 11, and 19-23, check your answers with PPLANE.

Week 5

Quiz on Thursday 2/15

The quiz will be on one or more of the following items.

• Problems # 3 p. 32, # 4 and 5 p. 33, # 8 and 9 p. 34, # 16 p. 36.
• Reading assignment: Section 12.4 of the notes (starting on page 133) on eigenvalues and eigenvectors, and Section 14.6 (starting on page 158) on phase plane analysis.

Week 4

Quiz on Thursday 2/8

The quiz will be on one or more of the following problems.

• Problems # 1 p. 32, # 12 and 13 p. 35, # 14 and 15 p. 36.

Week 3

Due Tuesday 1/30

In-class initial presentations. Prepare a 5-minute presentation describing your group and your project. You should cover all of the topics mentioned in the following template.

• Cover slide: title of your project, your names, your mentor's name.
• First slide: description of your team, who is doing what (remember roles and responsibilities may change throughout the semester). Indicate when your team meets, both on its own and with its mentor.
• Second slide: what the project is about (include contextual information as well as specifics), the articles you are using (include full references).
• Third slide: describe the type of model used in the articles, the hypotheses, and the type of approach used to explore the model (analysis, numerical solution, etc).
• Fourth slide: describe the results presented in the articles.
• Fifth slide: indicate what you plan to do for your project. In particular, describe your plans for working through the derivation of the model and testing it, list the results you would like to reproduce, mention whether you intend to explore how certain parameter values affect the model, or add new terms to the model in order to take new effects into account.

Also, place a PDF copy of your presentation in the D2L folder called Initial Presentation. The folder will close at 2 pm on 1/30.

Quiz on Thursday 2/1

The quiz will be on the material discussed in class and/or one or more of the following problems.

• All of the problems assigned so far.
• Problems # 6 p. 8, # 5 p. 15 and # 7 p. 16.

Week 2

By Tuesday 1/23

You should have done the following:

• Met with your mentor as a group.
• Identified a time of the week when your group will meet with your mentor during the semester, and when your group will meet on its own.
• Assigned roles within your group; examples of tasks include taking notes during meetings and sending a summary to the group; coordinating input from each group member; searching the literature and summarizing findings; coding up a numerical simulation; drafting your next presentation; working through the derivation of some equations and sharing your understanding with the group; submitting reports and presentations to D2L on behalf of the group; proofreading the final report. These roles can change or evolve throughout the semester but at the end of each meeting, it is important that everyone knows what they need to have accomplished before the next group meeting.

Quiz on Thursday 1/25

The quiz will be on one or more of the following problems.

• Problems # 1, 2, 3, 4, and 6 p. 15. Links to the articles mentioned in Problem # 6 are below. As usual, you will need to use your UA credentials to access the full text of these articles.
• Mexican waves in an excitable medium
• Human waves in stadiums

Week 1

Due Tuesday 1/16

Fill out the Project Preferences survey in D2L.

Install MATLAB on your laptop and bring it to class. If you prefer to program in Python or C, this is fine as well.

Due Thursday 1/18

Please place a single file (PDF preferred) with your work on both assignments in the D2L Assignment Submission Folder called Homework 1.

Assignment 1

Read at least two of the news articles below. Note: you need to be on campus or use the UA VPN to access the full text of some of these articles.

• Rapid Response Could Have Curbed Foot-and-Mouth Epidemic by M. Enserink
• Disease control: Virtual plagues get real by V. Gewin
• African swine fever outbreak alarms wildlife biologists and veterinarians by Erik Stokstad
• U.K. expands kill zone for badgers in fight against bovine TB, sparking controversy by Erik Stokstad

Then answer the following questions; include a discussion of the articles you read in your argumentation.

• Do you believe mathematical models should be used to make decisions that impact society?
• What criteria do you think such models should satisfy, if they are to be used for policy-making purposes?

Your essay should be about 1 page long, typed, and written in proper English. It will be graded for content as well as for writing style, spelling, and grammar.

Assignment 2

Problems # 5 p. 7 and # 7 p. 8. For information on the MATLAB fitting toolbox, please see https://www.mathworks.com/help/curvefit/index.html.

If you don't want to type up formulas, write down your solution of problem 5 on a piece of paper, scan it, and combine it with the rest of your assignment.