# BIOL398-03/S13:Class Journal Week 6

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## Contents

- 1 Laura Terada Week 6 Journal
- 2 Kevin McKay week 6 Journal
- 3 Kasey O'Connor Week 6 Shared Journal
- 4 James P. McDonald Week 6 Journal
- 5 Matthew E. Jurek Week 6
- 6 Anthony J. Wavrin Week 6
- 7 Elizabeth Polidan Week 6 Shared Journal
- 8 Paul Magnano
- 9 Salman Ahmad 6 Shared Journal
- 10 Helena M. Olivieri 6 Shared Journal
- 11 Ashley Rhoades Week 6

## Laura Terada Week 6 Journal

### Questions

- What was the purpose of this assignment?
- The purpose of this assignment was for us to think about what we want to do for our research project. We narrowed down a topic and identified two outside sources.

- Which project is easiest? Why?
- The third option might be the easiest because it's only factoring one other variable, the ammonia feed.

- Which project is hardest? Why?
- I think 4 is the hardest because it asks to develop a model of a ammonia sensor. This requires us to think about 2 nitrogen sensors, which I think might be difficult to think of.

- How might you tweak/revise/recreate the matlab codes we've developed to analyze your model?
- We will probably have to introduce new variables and set of equations if we want to factor in another component of the system.

Laura Terada 00:59, 22 February 2013 (EST)

## Kevin McKay week 6 Journal

- The purpose of this assignment was to use the skills we have been practicing over the last few weeks in modeling and analyzing bioogical systems.
- Personally I find none of them to be easy, I am not great at math modeling.
- Number 4 Seems to be the hardest one because that is the one I would find hardest to begin.
- I am going to have to tweak the differential equations so I get more accurate graph results.

Kevin Matthew McKay 14:04, 21 February 2013 (EST)

### Questions

- What was the purpose of this assignment?
- This assignment allowed us to begin to think about our project topic. It also gave us the opportunity to find sources other than the original terSchure papers so we have more information to be able to completely understand our topic.

- Which project is easiest? Why?
- I think they all seem to have a challenging, however, I think project three is the easiest. It only requires looking at the ammonia feed, and just altering the current models we have from per cell to per chemostat.

- Which project is hardest? Why?
- I think project two might be the hardest. From what we discussed in class, it would require having an in depth knowledge of anaerobic and aerobic reactions in yeast, as well as how to model the reactions based on the amount of glucose.

- How might you tweak/revise/recreate the matlab codes we've developed to analyze your model?
- We will have to determine the constant to keep the ammonia feed rate at, and then run tests at different dilution rates to see what happens to the model. We can look at the changes made to the model and graphs if the rate coming in is different than the rate coming out.

Kasey E. O'Connor 18:26, 21 February 2013 (EST)

## James P. McDonald Week 6 Journal

- What was the purpose of this assignment?
- The purpose of this assignment was to obtain resources that will aid us in our modeling project. It presents a starting point for us and got us to choose which project we would like to work on.

- Which project is easiest? Why?
- All of the projects seem difficult as math modeling is difficult for me, but I would have to say 3 looks easiest at first glance as you only have to account for one variable, the ammonia concentration.

- Which project is hardest? Why?
- The fourth project seems the hardest because you have to account for a two-component sensing system and I am unsure how I would begin on that.

- How might you tweak/revise/recreate the matlab codes we've developed to analyze your model?
- We will have to add new equations to the chemostat model to account for the oxygen consumption and carbon dioxide production.

James P. McDonald 21:19, 21 February 2013 (EST)

## Matthew E. Jurek Week 6

- What was the purpose of the assignment?
- The purpose of this assignment was to get us thinking about our project. This was a three-step process. First we had to decide on which of the four projects we'd be working on. Not only that, we had to think about what approach we would take regarding the specific problem we chose. Then we had to find a biologically relevant source that will hopefully help us fill in any missing pieces of information needed to complete our system of equations. Lastly, we had to look for a mathematical reference that will help us in the technical aspect of modeling the scientific process we've chosen.

- Which project is easiest? Why?
- I don't think any of them are easy. The idea of modeling is somewhat overwhelming for me. After looking at the project prompt I find myself asking where to begin on all of them. However, in class today we spent some time on the third project which helped me realize how/where to start on that one.

- Which project is hardest? Why?
- I think the fourth project is rather difficult. When dealing with a two-component regulatory system, there is obviously two components. This means that something triggers a chain reaction. There's a sensor that senses and outside factor which then triggers some intracellular reaction. I think it would be hard to factor all of these things into a model since there are so many moving parts.

- How might you tweak/revise/recreate the matlab codes we've developed to analyze your model?
- As mentioned in my journal. A few additional things need to be considered to properly model the third project. We will be incorporating the influx within the chemostat. This will be added to the dni/dt equation that was derived in class today. We also feel that the large amount of glutamate seen in the figures of the paper is due to something outside of the conversion reactions discussed in class. To account for this, we will be including this additional glutamate source into the dx/dt equation derived in class. This will require outside research to fully achieve what we hope to model.

**Matthew E. Jurek 23:44, 21 February 2013 (EST)**:

## Anthony J. Wavrin Week 6

- What was the purpose of this assignment?
- The purpose of this assignment is to have us get comfortable looking at scientific literature as a source. Additionally, creating our model for our presentations will be a combination of math skills and biological understanding. There will be information about yeast and their functioning that is necessary to know in order to create an accurate model, thus we will have to resort to this literature to find this information.

- Which project is easiest? Why?
- I believe project 1, terSchure and coauthors (Microbiology, 1995, 141:1101-1108) considered other conditions, such as changing the dilution rate. Apply our chemostat model to these conditions, is the easiest because it is more of an exploratory project. There is already a model made, it is just changing the parameters of that model. This does not require a deep level of thinking to type in the different values.

- Which project is hardest? Why?
- I believe project 4, The last line of the terSchure paper is as follows: “If the ammonia concentration is the regulator, this may imply that S. cerevisiae has an ammonia sensor which could be a two-component sensing system for nitrogen, as has been found in gram-negative bacteria (4).” Develop and analyze a model based on this concept, is the hardest because we do not have any foundation of this model. The other ideas we have played with in class and discussed. Project 4 is a project from scratch and requires a deep level of understanding on the biological side, what is really happening in this two-component sensing system, and in math, creating the working model from nothing.

- How might you tweak/revise/recreate the matlab codes we've developed to analyze your model?
- Luckily we have quite a bit of code written in matlab. Simply changing in a constant parameter with a different set of values will be the easiest way to attempt to tweak the codes. Also, using the Michaelis-Menton type of modeling will help in adding new components to the model.

Anthony J. Wavrin 23:56, 21 February 2013 (EST)

- What was the purpose of this assignment?
- This assignment got us thinking about our projects. It also pushed us to begin finding both biology/biochemistry and math resources to help as we develop and implement our model.

- Which project is easiest? Why?
- The first project seems easiest because all one must do is vary the ammonium concentrations.

- Which project is hardest? Why?
- The fourth project has the potential of being the most difficult. It is so open ended and one could get lost.

- How might you tweak/revise/recreate the matlab codes we've developed to analyze your model?
- I have to figure out how I am going to modify the set of equations to reflect a two-component sensing system. I have a ways to go before I can give more details.

Elizabeth Polidan 00:48, 22 February 2013 (EST)

## Paul Magnano

### Questions

- What was the purpose of this assignment? The purps of this asignmnt was to help us bgin our project by forcing us to fnd and analyze two sources for the topic we picked.
- Which project is easiest? Why? The third choice only has one additional variable, ammonia feed so fee like that would be the easiest.
- Which project is hardest? Why? The fourth choice asks you to consider 2 different nitrogen sensrs, a subject we havent talked about, so I feel like that would be the most difficult.
- How might you tweak/revise/recreate the matlab codes we've developed to analyze your model? We might add a fourth eqution to our script (incorperating the previous three for nitrogen, carbon, and yeast) to account for oxygen consumption and carbon dioxide production.

Paul Magnano 01:00, 22 February 2013 (EST)

### Questions

- What was the purpose of this assignment?
- The purpose of this assignment was for us to decide what project we wanted to work on. It was also useful to learn how to find papers to help us with specific topics in our projects.

- Which project is easiest? Why?
- All the projects seem like they will be difficult, but the third one might be a little bit easier because we went over parts of it in class today.

- Which project is hardest? Why?
- The fourth project seems like it could be the hardest. It involves developing and analyzing a new model for the concept. I don't think I could develop a brand new model and get it to work in MATLAB yet.

- How might you tweak/revise/recreate the matlab codes we've developed to analyze your model?
- We will have to change the MATLAB variables to try out the different conditions that our project requires. The code should stay the same because all the formulas are the same, but the values of the variables (the concentrations in particular) will have to be changed.

Salman Ahmad 01:41, 22 February 2013 (EST)

- What was the purpose of this assignment?
- The purpose of this assignment was to encourage us to delve further into scientific paper analysis and research. Through this assignment we were also encourage to hone in and begin the preparation process for presentation.

- Which project is easiest? Why?
- I find all of the projects slightly daunting for various reasons. I'm not sure I could identify a single one as the easiest. I suppose, any of the first three would be the easiest because we have worked through various aspects of each in class.

- Which project is hardest? Why?
- The fourth project seems to be the most open-ended and likely the most difficult because it requires the development of a completely original model.

- How might you tweak/revise/recreate the matlab codes we've developed to analyze your model?
- We will be manipulating the current chemostat models and, thus, codes, in order to account for the effects of a possible fluctuating dilution rate.

Helena M. Olivieri 02:01, 22 February 2013 (EST)

## Ashley Rhoades Week 6

### Questions

- What was the purpose of this assignment?
- The purpose of this assignment was to explore outside surfaces for our coming presentations.

- Which project is easiest? Why?
- The first project is easiest because the model is altered less and there is a specific source to guide the model.

- Which project is hardest? Why?
- THe fourth project looks more difficult because it is less guided and a new model needs to be made.

- How might you tweak/revise/recreate the matlab codes we've developed to analyze your model?
- We will have to tweak the dilution rate as well as the units to make sure bringing information from both articles works.

Ashley Rhoades 21:16, 25 February 2013 (EST)