User talk:Kpl21/Benchmark II: Model Description

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Student Comments

I think this model descirption is very well written. It talks about what going to be the output, what situation Lu wants to simluate. The state variables and terms are well explained. The parameter changes also indicated. There will be no problem to replicate the work or interpret the output.

The disadvantge is that the parameter changes are not well explained. This model description actually the method section of the journal. Each parameter change has its own meaining that needed to be clarified. However, it seems that Lu didn't talk about it. This left confusion about this part, reader won't understand the mechanism of this model. On this pint, I think example articles have some responsibility, the articles are so nicely written causes many people think the model description must be brief. Actually, contains everything is the pirority one, not neat.

--Ziyue Yi (talk) 13:31, 5 April 2017 (EDT)

A nice description, but could use some organizational help. Assumptions are easily listed as bullet points, and as stated above parameters are not well explained. Overall, it could use a bit more text to help explain each section in greater detail.

--Jessica Nash (talk) 12:35, 18 April 2017 (EDT)

Instructor Comments

  • Benchmark submitted on time?
    • No Yes
  • Rubric submitted on time?
    • Late (after 12:45 PM deadline) Yes
  • State variables, parameters and inputs to the model clearly distinguished?
    • Yes, but the titles in your table are misleading. You have a heading that says “State Variable Initial Condition”; this heading should be “State Variables”. You have a heading that says “Value”; this should be “Initial Values”. It would probably be better to put the state variable and parameter tables first.
  • Term-by-term description of model components?
    • Please check for clarity in your writing. For example, under equation 10, you say “This is an equation represents how the obtain the kwee constant.” You probably mean to say “This is an equation that represents how to obtain the kwee constant.” Careful proofreading will be important. Your attempts to describe the terms could also be much clearer. For example, in describing the first equation, you are correct that the equation using mass-action kinetics and that it finds the rate of change of the concentration of cyclin. But your description of the specific terms is too vague. For example, you could have said “Cyclin becomes available at a zeroth order rate of k1, is degraded in a first order reaction at a rate k2 as a function of its current concentration, and also is consumed in a second order reaction dependent on the CDK concentration at a rate k3.”
  • Have you described model assumptions?
    • You say “The initial differential equations using mass-action kinetics were initially replicated with Michaelis-Menten kinetics”. You are confounding two different assumptions. Your description of other assumptions could be clearer.
  • Description of equation simulation?
    • Your description of the equation simulation process is vague and unclear.

On the whole, this is a fair to good first draft of the model description section. Improving it along the lines suggested above could make it excellent. It will also need to be modified to incorporate the details of the model extension.

--Hillel Chiel (talk) 12:25, 9 April 2017 (EDT)