BIOL398-05/S17:Class Journal Week 10

Nika Vafadari Reflection Questions

Nika Vafadari

1. Overall, do you think this paper was clearly written? Why or why not?
2. Based on what is written in the methods section, do you think you could reproduce their experiments/models and data analysis?
3. What else would you like to know about their methods, results, and future directions?

Acknowledgments

• I certify that this individual journal entry was completed by me and not copied from another source.
  • Nika Vafadari 22:38, 29 March 2017 (EDT):

Margaret ONeil Reflection Questions

1. 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.

2. 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.

3. 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.

Acknowledgments

• I certify that this individual journal entry was completed by me and not copied from another source.

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

Lauren M. Kelly Reflection Questions

Lauren M. Kelly

1. 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.
2. 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.
3. 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.

Acknowledgments

• I certify that this individual journal entry was completed by me and not copied from another source.

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