Identify how the author addressed the steps of the model building process in the paper based on the guide below. (You don’t need to identify every single bullet point. They are included to provide a better picture of what each step means in general. E.g., as Step 1 figure out what the main question in the paper is. What is the hypothesis that the author explores?)

Constructing a Model

Step 1: Formulate the question

  • What do you want to know?
  • Describe the model in the form of a question.
  • Boil the question down!
  • Start with the simplest, biologically reasonable description of the problem.

Step 2: Determine the basic ingredients

  • Define the variables in the model.
  • Describe any constraints on the variables.
  • Describe any interactions between variables.
  • Decide whether you will treat time as discrete or continuous.
  • Choose a time scale (i.e., decide what a time step equals in discrete time and specify whether rates will be measured per second, minute, day, year, generation, etc.).
  • Define the parameters in the model.
  • Describe anyIdentify how the author addressed the steps of the model building process in the paper based on the guide below. on the parameters.

Step 3: Qualitatively describe the system

  • Draw a diagram to describe changes to the variables over time.
  • For models with many possible events, construct a table listing the outcome of every event.

Step 4: Quantitatively describe the system

  • Using the diagrams and tables as a guide, write down the equations.
  • Perform checks. Are the constraints on the variables still met as time passes? Make sure that the units of the right-hand side equal those on the left-hand side.
  • Think about whether results from the model can address the question.

Step 5: Analyze the equations

  • Start by using the equations to simulate and graph the changes to the system over time.
  • Choose and perform appropriate analyses.
  • Make sure that the analyses can address the problem.

Step 6: Checks and balances

  • Check the results against data or any known special cases.
  • Determine how general the results are.
  • Consider alternatives to the simplest model.
  • Extend or simplify the model, as appropriate, and repeat steps 2-5.

Step 7: Relate the results back to the question

  • Do the results answer the question?
  • Are the results counter-intuitive? Why?
  • Interpret the results verbally and describe conceptually any new insights into the biological process.
  • Describe potential experiments.