BIOL398-05/S17:Class Journal Week 10

Nika Vafadari Reflection Questions

While some of the mathematical equations were initially confusing to understand, especially when it came to determining the use of specific variables, the paper was clearly written in that it discussed the purpose of each equation and step very well in order to tie it into the big picture.
While the big picture was discussed well, the methods when it came to what was entered into each step of the equations was not discussed well, therefore I do not think I could entirely reproduce the experiment/ model.
I would like to know how they went about creating the various equations for the model, for example how closely related are these equations to the linear model and how do we trust that the equations correctly model what they state they are modeling.

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- Nika Vafadari 22:38, 29 March 2017 (EDT):

Overall, do you think this paper was clearly written? Why or why not?
I don't think this paper was very clearly written, because even though I have a pretty solid handle on graph statistics, and how networks operate, I often found myself having to re-read sections up to 5 times to understand what the authors were saying, which I feel impeded my work.
Based on what is written in the methods section, do you think you could reproduce their experiments/models and data analysis?
If given access to the raw data, I think reproducing their results would be fairly easy, with the exception of the distinct cycle lengths because I'm still not entirely sure how that measure was calculated. Otherwise everything was very well laid out in their methods.
What else would you like to know about their methods, results, and future directions?
I'd like to know if basin entropy and distinct cycle length are measures that can be calculated for non-Boolean networks, and if they can't, if the authors know of any comparable measures for general regulatory networks because it might be interesting to apply those measures to the 6 families of networks to continue investigating their structure and function.

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Margaret J. Oneil 23:14, 29 March 2017 (EDT)

Overall, do you think this paper was clearly written? Why or why not?
- This paper was clearly written in some areas and confusing in others. The methods and analytical methods were very clearly stated, therefore it was easy to follow what they were doing in the experiment. It became less clear when they began bringing in results from other papers into their discussion. I was able to figure out what they were saying, but the variety of information they were presenting all at once was daunting at first.
Based on what is written in the methods section, do you think you could reproduce their experiments/models and data analysis?
- I am unsure if I could reproduce this experiment. While I know that they grew the yeast in four different environments, it is unclear how many replicates of each environment there were, or if there even were any. I believe that I would be able to reproduce their experiment with further, more detailed investigation into what they did.
What else would you like to know about their methods, results, and future directions?
- I would like to know if they had any replicates of the glucose-limited/12°C, glucose-limited/30°C, ammonium-limited/12°C, and ammonium-limited/30°C chemostats. I would also like to know which genes in Figure 4 encode transporters, because the paper does not specify.

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Lauren M. Kelly 23:43, 29 March 2017 (EDT)

Overall, do you think this paper was clearly written? Why or why not?
- The paper was easy to understand in the introduction section and the materials and methods section. I was able to understand what they were going to be doing and how they were going to evaluate their results. However, the paper started to get confusing as I attempted to interpret the results and the discussion of the paper. The fact that there were so many tables and figures and that it referenced many other papers made it difficult to interpret.
Based on what is written in the methods section, do you think you could reproduce their experiments/models and data analysis?
- Based on what is written in the methods section, I think I would be able to reproduce the experiment. They grew the S. cerevisiae in a chemostat at 12°C or 30°C, limited the ammonium or the glucose, and kept all of the other variables constant across the different growth conditions.
What else would you like to know about their methods, results, and future directions?
- I'd like to know why they specifically chose the temperatures of 12°C and 30°C. Could there be other temperatures that would yield the same or better results?

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Cameron M. Rehmani Seraji 01:08, 30 March 2017 (EDT):

The paper was mostly clearly written. They explained their models in detail. The only problem I had was with the constant change of focus between figures. Instead of explaining one figure at a time the authors mentioned the figures briefly numerous times throughout the paper.
The methods did not nearly go into enough detail for me to replicate the experiment or the simulation.
I would like to know the criteria they used for narrowing their selection down to 184 regulators and 40 target genes.

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Conor Keith 02:36, 30 March 2017 (EDT)