User talk:Jxw773/Final Term Paper

From BIOL 300 Wiki
Jump to: navigation, search

Student Comments

These bullet points go in the paper (earlier notes are on intro, later notes on discussion):

  • Handle is a vague world, for a while I was using that to describe the relationship between bacteria and neutrophils too, but I think replacing "handle" with "eliminate" or "protect against" is more specific.
  • Neutropenia is not just a developed condition (like in the case of chemotherapy that you mention), it is also congenital, and you should probably mention that.
  • Experimental data was from Li et. al., not Malka. et. al.
  • You describe what Type I and Type II dynamics are in paragraph two, but never actually mention the term.
  • You say the extension is "either the neutrophil or bacterial influx as a state variable" but we extended the model with just neutrophil influx. You should probably definitively state that, and mention influx in discussion.
  • Consider making a separate table for extension parameters.
  • Remember to explain how we changed the fourth assumption for our extension.
  • Just a formatting tip: "System 1" appears in a box, "System 2" does not.
  • Consider adding more detail about extension simulations.
  • Your results look great. Remember to add the figures we made.
  • The first sentence of Discussion says "The hypothesis was..." but really it was the hypothesis of Malka et. al., and you don't want the reader to mix up our extension hypothesis with the hypothesis from Malka et. al.
  • Remember to move where the Neutrophil Influx equation is

So far your paper looks great! --Tate Keller (talk) 16:48, 30 April 2017 (EDT)

Please paragraphing and improve the phrases in your article, the huge bulk of words is not easy to understand. I hope this is because the article is still in construction.

From the brief reading of your article, I noticed it is a bifurcation analysis of immune cells versus the bacteria. At this moment the finish level is pretty low.

In introduction, there is no mention about the main point that is what is type I and II dynamics. In model description part, there is also no explaination about dynamics. I guess it is the system 1 and 2. However, the dynamics shows up in the result. This is a big problem because the backbone of the argument is the core of writing.

In result part, please start with the figure description, I used some time to figure out what the figure meaning.

For discussion part, I recommend you not to mention about the drawback of modeling. Instead, add some more about the current model, how is it compare to the other modeling techniques.

The reference is not correlates to your article. Be careful, many people assume a lot as common sense, and finally be asked to add the reference.

--Ziyue Yi (talk) 18:42, 30 April 2017 (EDT)

Instructor Comments

  • Term paper survey submitted with term paper?
    • Yes.


  • Significance of problem?
    • Yes.
  • Statement of hypothesis?
    • Yes.
  • List of references?
    • Yes; 8 of 11 cited in the Introduction; many are more recent than the original paper. More references and discussion of them would have strengthened the Introduction.
  • Properly formatted references?
    • Yes.

Model Description

  • State variables, parameters and inputs to the model clearly distinguished?
    • Yes.
  • Term-by-term description of model components?
    • Yes.
  • Have you described model assumptions?
    • Yes, very clearly.
  • Description of equation simulation?
    • Yes; more details should have been provided. Derivations of the equations that provided the borders for the graphs should have been clearly explained. 7


  • Results described and compared to original paper?
    • Yes.
  • Have you addressed the original biological hypothesis?
    • Yes.
  • Figures and legends to show results?
    • Yes.
  • Discrepancies relative to original model?
    • Yes.
  • Uploaded Mathematica file?
    • Yes.


  • How well does the model support the original hypothesis?
    • Well discussed.
  • Support for hypothesis and assumptions from other data in the literature?
    • Some support provided; more would have been better.
  • Limitations of results?
    • Good discussion of limitations.
  • Discrepancies and how they affect conclusions?
    • Well discussed.
  • Relationship to other work in the field?
    • Mentioned in the introduction, not really expanded upon very much in the Discussion.
  • Discussion of future work?
    • Some discussion of future work. More literature citations and thoughtful discussions of the implications of that literature would have greatly strengthened this section

Overall Term Paper Quality

  • How well was the model replicated?
    • An excellent job of replication.
  • Based on the term paper, how well did you understand the material?
    • Understanding is excellent.
  • How well written is the term paper?
    • Some textual errors. For example, in the Introduction: “…there was a range between the two critical values in which the neutrophil levels could control a range of low bacteria concentrations but high bacteria concentrations.” The word “not” is missing before the word “high”. Here is an example of a sentence fragment from the Discussion: “As seen on figure 3, within the assumptions type II dynamics covers a larger range of parameter values than type I dynamics.”. There are small typographical errors, and some sentences should have been clarified. However, on the whole, the paper was quite clear and understandable.
  • How hard was the model extension that you did?
    • A moderately difficult extension, involving creating a whole new equation and changing the dimensionality of the model from 1 to 2 dimensions.
  • How good was the extension?
    • Quite good. Using phase plane analysis, you were able to get some insight into how the model would work under these more complex conditions.
  • Mathematica code clear and well annotated?
    • Yes.
  • Mathematica code generates figures when evaluated?
    • Yes.

On the whole, this is a very good to excellent term paper; there are some weaknesses in the writing, and the discussion section could have been much stronger, but every other part of the paper is excellent, including the extension and the Mathematica code. Nice work!

--Hillel Chiel (talk) 09:03, 12 May 2017 (EDT)