Talk:CH391L/S14/Oscillation

Comments
--drewtack (talk) 14:35, 24 March 2014 (CDT)Just starting with the introduction. I'm not entirely sure that you're introduction is appropriate for the subject matter; you should probably focus on biological or synthetic biology oscillations immediately.
 * --Dennis Mishler (talk) 11:57, 25 March 2014 (CDT) Related to Drew's comment, Ashley I would like to see an actual introduction. What are oscillators?  What is oscillations?  I think you can then go into the descriptions that you already included.
 * --Ashley Kessel (talk) 11:37, 31 March 2014 (CDT) I revised the introduction drastically, hopefully it fits the criteria.
 * --Dennis Mishler (talk) 12:04, 25 March 2014 (CDT) I've never heard of this before... Is this a typo?: "Entertainment is defined as the systematic process of synchronization of the biological network."
 * --Ashley Kessel (talk) 11:37, 31 March 2014 (CDT) Thats not a typo, but I did change where I put that text to make it more relevant.
 * --Dennis Mishler (talk) 12:04, 25 March 2014 (CDT) In Biochemical Oscillations, you introduce A LOT of big words/concepts. “negative feedback, time delay, sufficient ‘nonlinearity’ of the reaction kinetics and proper balancing of the timescales of opposing chemical reactions.”   Are you going to refer to these in the future, or give examples, or somehow relate back to these terms later?
 * --Ashley Kessel (talk) 11:37, 31 March 2014 (CDT) I thought it would be good to know what a synthetic oscillator is, even if I do not specifically refer to the same terminology later. I did define the terms more in depth.


 * --Dennis Mishler (talk) 12:09, 25 March 2014 (CDT) Grammar in the last sentence (maybe a typo) of the repressilator section needs to be fixed.


 * --Alejandro Gutierrez (talk) 06:25, 28 March 2014 (CDT) For the future directions section, is it possible to add an example of how the oscillators may be used, in a complex circuit or otherwise? I know it is sometimes difficult to find literature on the more complex theoretical circuits, but if you could find one or two examples, it would help my understanding of the subject.


 * --Liz (talk) 07:22, 28 March 2014 (CDT) Agree with above statements about introduction- it seems colloquial and disjointed. Better transitions would help tie the ideas together.  Also I think it would be really helpful here to have an figure illustrating the idea of an oscillator and how it functions/can be described- can you find something like that in a review? Why does the "entertainment" belong in this section? I'm not getting much from the biochemical oscillator section.  Like we discussed in class, it would help to relate the terms of the equation to real life variables, or if you can't do that exactly at least make some explanation of why it was found to be a valid equation.  Some more detail about the behavior of the biochemical oscillators you mention would be helpful- even going into detail (ie explaining how one fits the parameters you mention at top) for one and listing the others would be an improvement. Agree with Dennis that the wording of your Repressilator section could be cleaned up and clarified. I would resize your figure if possible to match the width of the article. As far as captions go, I would say list them as citations and just have the number at the end of your caption, not the whole link right in there.
 * --Ashley Kessel (talk) 11:37, 31 March 2014 (CDT) I fixed the introduction, a lot of the "real life variables" introduce a lot of math that involves statistical physics which I am unfamiliar with, however I did mention how the rate of certain processes will effect the frequency and so forth in the math section.

--Dennis Mishler (talk) 12:50, 28 March 2014 (CDT) Chen's Wiki Critique

Overall Format and structure: The overall structure of this wiki page is good. It starts with the general introduction of oscillation, and how oscillation is related with a biosystem. The two examples of synthetic oscillation systems are very informative and easy to understand. However, the math of oscillation is not really connected well with the oscillation system, so I suggest it should be put in the introduction section, after the first paragraph, instead of at the end of the wiki page.

Introduction and background material: First I am not sure why mentioning entertainment in the second paragraph? I like the example of the sheep. It shows how oscillation can also happen in a bigger scale. But it will connect the idea of oscillation with biology better if you can have more similar examples to explain how oscillation can nature occurs in biology, not only in molecular scale, but also in a larger scale. For example, the population of a species can be oscillating with the population of its predator. Also, you mentioned some nature oscillators like AMP, so maybe you want to add few more sentences or a figure to describe one of them as an example. One minor things: I though “et al” should always followed by a period?

Methods and main body/concepts: In the first example, you mentioned the system is not stable or with noise. I think it will be helpful to show the results they had in the paper, so the readers can understand how the system turns into unstable or how the noise can affect the oscillation. In the second example, I have a question about how to use IPTG or arabinose to control the period. I thought their concentration should also fluctuate with oscillation. For the math model, we know the oscillation can be over damped or critical damped. But I am not sure how this is related with the biology oscillation systems. How can this fact help us to design a better oscillator?

Relation to iGEM and future directions: In the future direction section, I want to see more examples about the current study of oscillators, and how people use oscillators to help them build a better gene network in synthetic biology.

Figures, Figure legends, and citations: The figures are all very easy to understand and well explained. The citations are fine, but as I mentioned above there can be more citations about recent studies.