BIOL368/F20:Week 2

This journal entry is due on Thursday, September 17, at 12:01am Pacific time.

Overview

The learning objectives for this assignment are:

• To explore an interactive model of disease transmission.
• To practice documenting your scientific workflow in the service of reproducible research.

Individual Journal Assignment

Homework Partners

• You will be expected to consult with your partner, in order to complete the assignment.
• Each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed).
• You must give the details of the interaction with your partner in the Acknowledgments section of your journal assignment.
• Homework partners for this week are:
  • Fatima & Aiden
  • Nathan & JT
  • Owen & Anna
  • Macie & Yaniv
  • Taylor & Kam
  • Nida & Ian

Format and Content Checklist

1. Store this journal entry as "username Week 2" (i.e., this is the text to place between the square brackets when you link to this page).
2. Write something in the summary field each time you save an edit. You are aiming for 100%.
3. Invoke the template that you made as part of the Week 1 assignment on your individual page. Your template should contain:
   • A link to your user page.
   • A link to the template page itself.
   • A list or table of all of the Assignment pages for the course.
   • A list or table of all of your individual journal pages for the course.
   • A list or table of all the shared class journal pages for the course.
   • The category "BIOL368/F20".
4. Purpose: a statement of the scientific purpose of the assignment. Note that this is different than the learning objective stated on the assignment page. What science will be discovered by completing this assignment?
5. Combined Methods/Results (Electronic Lab Notebook): documentation of your workflow for this exercise. It should include:
   • The protocol you followed in enough detail for someone else to be able to conduct the same investigation. There should be enough detail provided so that you or another person could re-do it based solely on your notebook. You may copy protocol instructions on your page and modify them as to what you actually did, as long as you provide appropriate attribution.
   • Answers to any specific questions posed in the exercise.
   • Screenshots and images to document your answers.
   • Data and files: links to all data and files used and generated (you don't need to include images in this list).
     • Files left on the Desktop or My Documents or Downloads folders on the Seaver 120 computers will be deleted upon restart of the computers. Files stored on the T: drive will be saved. However, it is not a good idea to trust that they will be there when you next use the computer.
     • Thus, it is a critical skill for data and computer literacy to back-up your data and files in at least two ways:
       • Upload the files to this wiki.
       • Upload the files to Box.
       • Back them up on your personal flash drive.
     • References to data and files should be made within the methods and results section. In addition to these inline links, create a "Data and Files" section of your notebook to make a list of the files generated in this exercise.
6. Scientific Conclusion: a summary statement of the main result of exercise/research. It should mirror the purpose. Length should be 2-3 sentences, up to a paragraph.
7. Acknowledgments section (see Week 1 assignment for more details.)
   • You must acknowledge your homework partner with whom you worked, giving details of the nature of the collaboration. You should include when and how you met and what content you worked on together.
   • Acknowledge anyone else you worked with who was not your assigned partner. This could be the instructor, the TA, other students in the class, or even other students or faculty outside of the class.
   • If you copied wiki syntax or a particular style from another wiki page, acknowledge that here. Provide the user name of the original page, if possible, and provide a link to the page from which you copied the syntax or style.
   • If you copied any part of the assignment or protocol and then modified it, acknowledge that here and also include a formal citation in the Reference section.
   • You must also include this statement:
   • "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
   • Sign your Acknowledgments section with your wiki signature (four tildes, ~~~~).
8. References section (see Week 1 assignment for more details.)
   • Use the APA format.
   • Cite this assignment page.
   • Cite any protocols that you copied and modified (this must also be noted in the Acknowledgments section).
   • Cite any other methods, software, websites, data, facts, images, documents (including the scientific literature) that was used to generate content on your page.
   • Do not include extraneous references that you do not cite or use on your page.

Background

• Video: The role of applied math in real-time pandemic response: How basic disease models work
• The SIR Model: Using Math to Save the World: Math Can Predict the Spread of Infectious Diseases
• Giordano, G., Blanchini, F., Bruno, R., Colaneri, P., Di Filippo, A., Di Matteo, A., & Colaneri, M. (2020). Modelling the COVID-19 epidemic and implementation of population-wide interventions in Italy. Nature Medicine, 1-6. DOI: 10.1038/s41591-020-0883-7
• Schnell, S. (2015). Ten Simple Rules for a Computational Biologist’s Laboratory Notebook. PLoS Comput Biol, 11(9), e1004385. DOI: 10.1371/journal.pcbi.1004385

Tasks

This week, you will begin documenting your workflow in your individual journal entry. Refer to Schnell et al. (2015) for rationale and guidelines that professional computational biologists use. You need to describe what you did in enough detail that someone else can reproduce it using only your documentation. You may copy and modify these instructions, making sure to Acknowledge this properly and cite this page in your References section.

1. Watch the video: The role of applied math in real-time pandemic response: How basic disease models work
   • Record two questions that you have after watching the video.
2. Read the information on this website.
   • Look at the graphs and make sure you understand how to interpret them by answering the questions:
     1. What happens if initial I = 0?
     2. What does it mean that red line increases so rapidly?
     3. What does it mean that green line also rises rapidly, but not as rapidly?
     4. What does it mean that the green line reaches nearly to 1,000?
3. You will now explore an online, interactive SIR model, Epidemix.
   1. Go to the website and click the "Start" button in the middle of the page.
   2. Select the type of model you will explore from the drop-down menu on the upper-left side of the page. Explain why you made that choice.
   3. Take a screenshot of the initial plot that is shown on the page and display it on your individual journal page (remember, this will be a 2-step process to upload the image file and then display it on your page).
      • Describe in words what the graph is showing.
   4. Now you will explore the model by changing the parameters and seeing what happens to the graph.
      • Choose one parameter to change at a time. It will be helpful to make "extreme" changes so that you are sure to see a difference. You and your partner can collaborate and make different changes to the parameters and compare your results.
      • Make the change and display the plot on the Epidemix website.
      • Take a screenshot of the plot and display it on your individual journal page.
      • Describe in words what happened to the plot, thus interpreting the effect of the parameter change in the model.
      • Repeat this process 9 more times so that in the end, you will have 11 total screenshots. The initial conditions and 10 cases where you changed one parameter.
4. Look at Figure 1 of the Giordano et al. (2020) article.
   • How did the authors modify the simple SIR model to take into account features of the COVID-19 pandemic?
   • What public health policy implications does their model have?
5. Check your understanding: https://xkcd.com/2355/. Why is this comic funny? (Hint: hover your mouse over the graphic to see the extra joke in the tooltip.)
6. Write your scientific conclusion: a summary statement of the main result of exercise/research. It should mirror the purpose. Length should be 2-3 sentences, up to a paragraph.

Shared Journal Assignment

• Compose your journal entry in the shared Class Journal Week 2 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
• Create a header with your name, and then answer the questions in your own section of the page.
• You do not need to invoke your template on the class journal page.
• Any Acknowledgments and References you need to make should go in the appropriate sections on your individual journal page.
• Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
• Add the category "BIOL368/F20" to the end of the wiki page (if someone has not already done so).

Read

• Epstein, J. M. (2008). Why model? Journal of Artificial Societies and Social Simulation, 11(4), 12.

Reflect

1. Based on the reading by Epstein (2008), why should scientists model the COVID-19 pandemic?
2. Why did Dr. Dahlquist give this exercise?
3. Write three questions that you have about the COVID-19 pandemic or the SARS-CoV-2 virus that causes it. These questions can be about any aspect, they do not necessarily have to be about modeling.