Term paper proposal

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Each student must submit his or her own term paper proposal, even if the ideas were discussed by members of a team.

It is unacceptable to plagiarize.

This applies to all aspects of the term paper: the term paper proposal, the model plan, the Benchmarks, and the final term paper.

To be clear: if the text is not your own - if it is from an article, a website, any source other than your own mind - put it in quotation marks.

It is not acceptable for two or more students to make copies of the same text, and slightly modify the text, and hand in the resulting versions as their own.

Please see the rules and examples of Plagiarism.

Please submit the term paper proposal on your own page of the class wiki, using the Term Paper Template. Once you have done this to submit the term paper proposal, you do not have to do it again.

The term paper proposal - like all parts of the term paper - must also be submitted with a rubric that ensures that you have addressed the key issues necessary to ensure success in reconstruction. After finishing the term paper proposal, please fill out the rubric, and submit both the term paper proposal and the rubric at the same time.

The term paper proposal ensures that you have read the published paper describing the biological model with sufficient care that it is likely you will be successful in reconstructing the model.

If the rubric is not submitted, your term paper proposal will be considered late, and you may receive no credit for it.

In the rubric, as in the term paper proposal, you must address these questions (each can be addressed in approximately one detailed paragraph):

  • What biological hypothesis does the model test?
    • Note that the statement "It is possible to model (some biological phenomenon)" is not a meaningful or acceptable hypothesis, since it is always true.
    • A testable hypothesis, by definition, can be false.
    • For example: "Schooling will improve the chances that any member of a school will escape predation. This hypothesis will be tested by creating a model of schooling in fish, and the probability of survival will be measured in the presence of a predator when fish do or do not form a school."
  • Have you briefly described the model? This should include:
    • How many state variables are there in the model?
    • How many parameters are there in the model?
    • What are the assumptions underlying the model?
    • For example: "The model of osteoblast control involves fourteen state variables and twenty five parameters. The change with time of twelve of the fourteen state variables are described by twelve differential equations. The remaining two state variables are derived from an algebraic combination of the other state variables. All but three of the parameters are fully specified by data; the paper focuses on the effect of varying the three parameters on both the qualitative and quantitative behavior of the model."
  • How will you recreate the model? This should include:
    • What steps will you take to recreate each part of the model?
    • How will you ensure that each component that you build is correct?
    • What results will you reproduce from the published paper?
    • What extensions to the model will you explore, and how will you change the model to explore them?
    • For example: "To reconstruct the model of insulin regulation, we will first focus on the equations describing its metabolism within the pancreatic cells (equations 1 to 5). Once we have constructed this portion of the model, we will test its correctness by comparing the results we obtain to those shown in Figure 2 of the paper. We will then construct the portion of the model that represents the changes in blood levels of key metabolites that activate the pancreatic cells (equations 6 to 14). We will compare the results of the component of the model to those shown in Figure 3 of the paper. We will then "connect" the different components of the model together, and this should allow us to reproduce the data shown in Figures 4, 5, 6 and 7 of the original paper. The authors did not fully explore the effects of varying the parameter describing the breakdown of insulin, and we will explore the effects on the model of varying this parameter by a factor of ten. There are published results suggesting that reduced breakdown can lead to significant changes in circulating insulin levels, and we will compare published measurements of these levels to those predicted by the model."

Here is an exemplary project proposal that can help guide you as you write your own:

Filling out the hypothesis identification quiz will be worth 1/4 point towards the 50 points for the term paper.

If the term paper proposal is accepted, you will receive 3/4 point towards the 50 points for the term paper.

If the term paper proposal is not accepted, and needs to be revised, you will need to have it approved before you may proceed, but you may not receive any points for it.