The overall structure and content should contain the following:

1. Introduction to the biology
2. Your hypothesis to be addressed in the model you are making
3. The methods you are using to create the model (Stella, mass action, michaelis-menten, etc).
4. Model statements. These are statements like:
   cyclin is synthesized constantly; activation of MPF is dependent on cyclin binding to cdc2; etc.

1. Details of the model
   1. Changes in variables (your proteins) written as differential equations (dC/dt=V1-V2).
   2. The rate equations used for each reaction
   3. Any simplifying assumptions. What mathematical changes were made and why.
2. Methods of analysis, i.e.
   1. time course data (variables or rates over time)
   2. phase portraits (one variable in terms of another).

1. Figures: tables, graphs, concept maps
2. Description of results
3. Figures and descriptions go together
4. Include two of the following
   1. Results compared to previous model
   2. Results based on changes in initial concentrations or parameters (rate constants or rate equations)
      1. Choose values that help to test your hypothesis
   3. Results compared to experimental data, i.e.
      1. choose a specific wet-lab experimental result to which to compare your data
      2. Find an experimental data set for your organism that you can analyze and compare to your simulation results
         

1. How do you think the results confirm or negate your hypothesis?
2. How are results dependent on your assumptions about the rate equations or the variables you chose to use or not use?
3. What critiques do you have of your own and the "original model"?

1. What types of analysis would address your critiques?
2. What types of information or experiments are needed for future research on your model?