# BIOL398-04/S15:Class Journal Week 3

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## Contents

## William A. C. Gendron

### Reflection

- What was the purpose of this assignment?
- To teach us to use MatLab. It really made us do a lot of our own research to figure out why certain aspects were not working when we thought they were suppose to.

- How might you adjust the chemostat program to use two nutrients?
- Add another variable that represents that nutrient. This would interact with cells, but should not be related to food directly. The changes in nutrients will effect the cells and the least nutrient will limit the colony. Therefore if there is a large amount of nitrogen and a small amount of carbon, the cells will grow to the point that amount of carbon allows.

- How might these equations relate to the journal club paper?
- The paper could create be used as an ideal system for a model. It would be much more complicated than these models, but it would be possible. If I were to direct such a project, I would like to see more repetitions of the experiment to make sure that the information was accurate.

**William A. C. Gendron 00:11, 3 February 2015 (EST)**:

## Lauren M. Magee

### Reflection

- What was the purpose of this assignment?
- The purpose of this assignment was gain experience in using Matlab script. We were given directions to create our own script and then we were given a more complex script so that we could see the process in running a simulation using Matlab. This practice will be invaluable as we continue on with our own projects of mathematical modeling.

- How might you adjust the chemostat program to use two nutrients?
- You would need to include another variable on the plot that represented another nutrient, besides "food" which is already included. You would define this new variable in the context of time and cell population, as well as note the rate constants and parameters. You would also need to add it to the Matlab plotting sentence that is already included in your previous script.

- How might these equations relate to the journal club paper?
- These equations relate to the journal club paper, because they are graphical representations of cell growth. Just as the paper represented, these graphs are models depicting the cell growth in comparison to time and presence of a nutrient. In the paper they were primarily focusing on ammonium presence instead of food, but the effect of the model is similar.

Lauren M. Magee 02:53, 3 February 2015 (EST)

## Karina Alvarez

- What was the purpose of this assignment?
- The purpose of this assignment was to familiarize ourselves with MATLAB, and practicing the different functions available to us.

- How might you adjust the chemostat program to use two nutrients?
- In this chemostat model, a general "food" was used. In order to use two nutrients in another chemostat, I would add another variable. I would consider making "food" more specific, as in using glucose and a nitrogen source as two different nutrients (just as in the paper we analyzed). This extra variable would have to be accounted for in the formulas modeling the chemostat and the growth of the cells.

- How might these equations relate to the journal club paper?
- These equations relate to the paper in that they model similar systems. They both use mathematical models to understand the consumption rates of organisms in a chemostat program.

**Karina Alvarez 00:26, 3 February 2015 (EST)**:

## Lucia I. Ramirez

### Reflection

*What was the purpose of this assignment?*

- The purpose of this assignment was not only to get some practice with Matlab, especially using the function command and plotting, but to also understand how to upload and create links on our openwetware page.

*How might you adjust the chemostat program to use two nutrients?*

- I would adjust the dynamic function

*How might these equations relate to the journal club paper?*

- The plots

Individual journal for Week 3

Lucia I. Ramirez 02:59, 3 February 2015 (EST)

## Kara M Dismuke

- What was the purpose of this assignment?
- I believe the purpose of this assignment was for us to become more familiar with Matlab, especially as it pertains to how we will use it in the future to learn how to model biological systems. Most specifically, there was a clear emphasis placed on learning how to plot data, which (I assume) will be necessary when we are asked to not just plot the data, but to actually analyze it.

- How might you adjust the chemostat program to use two nutrients?
- We can introduce another nutrient (new variable) whose affects can be tested using our equations. We can isolate the nutrients into different trials so that there is no way the two nutrients can affect each other. I suppose, however, we can also use two nutrients within the same trial if we were interested in seeing how the presence of both affects the output. From a modeling standpoint, the introduction of a new nutrient means that our equations must account for a new variable (if we are testing both nutrients at the same time).

- How might these equations relate to the journal club paper?
- Similar to the journal club paper which plotted experimental data to observe trends, we are creating plots to study trends that we observe. For this assignment, however, we clearly did not perform the experiment and thus had no data to plot; rather, we used mathematical models to predict the outcomes. In addition, just as with the journal club paper, we see a comparison of different trial runs, most notably with the final graph that graphs the food and cells from both runs.

## Tessa A. Morris

- The purpose of this assignment was to have us become more comfortable using Matlab to assist in analyzing mathematical models. This assignment also forced us to leave our comfort zones and figure out how to use Matlab, even if specific actions weren't explicitly explained to us.
- In order to have the chemostat run two nutrients, another variable could be added. It would still be plotted against cells, but would not be dependent on the other nutrient. It would be similar to the way that Figure 4 had different variables on the plot, which were summarized in the legend in the top right of the graph. When dealing with multiple variables it is important to be specific when labeling, or else it can become extremely confusing.
- These equations are a mathematical model of a biological system, similar to that of the journal club paper. In both cases, the model can be used to understand behaviors and make educated predictions about future behaviors. Modeling systems gives scientists an advantage when studying the effects of certain variables on a population. By analyzing graphs, scientists can adjust their predictions and experiments.

Individual Journal Assignment Tessa A. Morris 01:14, 3 February 2015 (EST)

## Kristen M. Horstmann

- I believe the main purpose of this assignment was to help us get familiar with MATLAB and the main functions within MATLAB that will be most applicable to Biomath (creating a graph, using logarithmic functions, etc.). By learning the more basic commands now- and the errors that can result- we will find using MATLAB for more complicated systems later much easier.
- I am a little confused by this question as the chemostat script does not specify which variables stand for what. By inspecting the script, function, and my notes, I will assume 'uy' is the nutrient value. Also, I am not sure if this question means two nutrients together in a function or separate. Either way, one would have to create a new variable for a second group of nutrients. One should create a new function for the variable to test how this same model is determined by the new nutrients, but use a different value for the output in order to differentiate the results vs each nutrient. Or, if one was trying to gauge how the nutrients worked together, one would need to add the new variable to the original nutrients variable.
- This assignment somewhat relates to the journal club paper as we are using a algorithmic program to create a mathematical model, much like the researchers in the article we read. By plotting the nutrient colony and chemostat models, we can predict specific outcomes in order to compare them to the actual experimental values we may be able to find. Also, much like in the journal club paper, we are using these models to predict the outputs of a chemostat.

## Natalie Williams

**What was the purpose of this assignment?**- The purpose of the assignment was to help us get familiar with MATLAB and writing some simple code. However, the term simple is subjective, because some of the steps and inputs were not always clear. For the remainder of the semester, I 'assume' that this program will be a big part of the course. To have a better handle on MATLAB we had to do the assignment.

**How might you adjust the chemostat program to use two nutrients?**- To use two nutrients, I would add an addition equation for the second nutrient depletion rate. Both of the rates would have to be measured and observed so that a differential equation would be given. Each of those rates, depending on if the cells prefer one over the other, would have their own parameters.

**How might these equations relate to the journal club paper?**- These equation might relate to the journal club paper because the authors could have used their method to graph their results. With a differential equation, multiple plots could have been made on a single display to make comparisons on an equal scale. Furthermore, the same settings could be applied with varying equations; in doing such, the results would be more comparable because we control the conditions. By altering the settings, predictions can be made to the model to see how it would react under different environmental stresses and conditions.

- Natalie Williams 00:57, 3 February 2015 (EST)

## Alyssa N Gomes

- What was the purpose of this assignment?
- The purpose of this assignment was to allow us to work constructively with MATLAB and get used to the programming of script. This assignment allowed us to go beyond what we learned in lecture and utilize the Matlab Help functions in order to help us get used to the trial-and-error method that is often required in both Matlab and Mathematica.

- How might you adjust the chemostat program to use two nutrients?
- In the chemostat program, if we used two nutrients, it would be hard to see how each nutrient affected the cell growth individually. It might be helpful to see each nutrient individually, but seeing as cells will need food, it would be hard to run the experiment with only whatever the other nutrient is. We may just have to use both nutrients together to get one output of cell growth. In which case, we would be adding the use of the other nutrient on the graph, but the cell growth would be altered by both nutrients.

- How might these equations relate to the journal club paper?
- These equations might relate to the journal club paper because we are using an algorithm to predict trends in growth and analyze several variables against each other. We are using graphical models and actual data in order to see whether there is growth, decrease, or an equilibrium of values.Putting the two different runs of different dilution values against each other on a graph allows us to make sense of a comparison of different values, something that the journal club paper attempted to do with the different gene encodings graphed on the same graph.

Alyssa N Gomes 23:59, 2 February 2015 (EST)

## Jeffrey Crosson

*What was the purpose of this assignment?*

- The purpose was to check, improve, and acquire our Matlab skills.

*How might you adjust the chemostat program to use two nutrients?*

- Add another variable into the chemostat dynamics script. Different differential equations would be necessary.

*How might these equations relate to the journal club paper?*

- They had to maintain and change certain nutrients in their experiments. These values change with respect to another changing value, therefore they also utilized differential equations.

**Jeffrey Crosson 5:57, 3 February 2015 (EST)**