# BIOL398-01/S11:Class Journal Week 4

(Difference between revisions)
 Revision as of 18:44, 6 February 2011 (view source) (→Alondra Vega's Journal Entry: added my signature)← Previous diff Revision as of 20:00, 6 February 2011 (view source) (→Alondra Vega's Journal Entry)Next diff → Line 55: Line 55: #The part of the assignment that came most easily to me was defining the terms.  I feel that they are more mathematically based than biology based, so even if I did not know what they meant, it cool to learn about them.  This section of the homework did not take me too long. #The part of the assignment that came most easily to me was defining the terms.  I feel that they are more mathematically based than biology based, so even if I did not know what they meant, it cool to learn about them.  This section of the homework did not take me too long. #The most challenging part of this assignment was working with matlab and trying to figure out how to put all the plots in the same graph.  I had never really worked in matlab and writing a code, so it was not very easy to navigate through the help menu.  Once I figured that out, running the code was simple. #The most challenging part of this assignment was working with matlab and trying to figure out how to put all the plots in the same graph.  I had never really worked in matlab and writing a code, so it was not very easy to navigate through the help menu.  Once I figured that out, running the code was simple. - #I still do not understand how the application comes in.  If it were not for the legends in the graphs, I would not have been able to figure out what the figures represented.  I feel that we are modeling concentrations, but I have a very strong feeling that i am wrong.  I do not understand what we are running and why it is important to us. + #I still do not understand how the application comes in.  If it were not for the legends in the graphs, I would not have been able to figure out what the figures represented.  I feel that we are modeling concentrations, but I have a very strong feeling that i am wrong.  I do not understand what we are running and why it is important to us.  I also don't understand the difference between the catalysis driver and the Michaelis-Menten product driver; I feel that they give the same product. [[User:Alondra Vega|Alondra Vega]] 17:44, 6 February 2011 (EST) [[User:Alondra Vega|Alondra Vega]] 17:44, 6 February 2011 (EST) [[Category:BIOL398-01/S11]] [[Category:BIOL398-01/S11]] [[Category: Biomathematical Modeling]] [[Category: Biomathematical Modeling]]

## Instructions

### Formatting

• Sign your portion of the journal with the standard wiki signature shortcut (`~~~~`).
• Add the "BIOL398-01/S11" category to the end of the wiki page (if someone has not already done so).

### Reflection

1. What was the purpose of this assignment?
2. What aspect of this assignment came most easily to you?
3. What aspect of this assignment was the most challenging for you?
4. What (yet) do you not understand?

## Class Responses

### Sarah Carratt's Journal Entry

1. The purpose of this assignment was to practice using the Michaelis Menten model and Matlab.
2. Finding Vmax and K was easiest for me.
3. Matlab remains the hardest part of the assignment for me
4. I keep getting error messages in Matlab that I have trouble correcting. It can be really frustrating and I feel like I won't ever understand it on the first try.

Sarah Carratt 17:22, 6 February 2011 (EST)

### James C. Clements' Journal Entry

1. The purpose of this assignment was to learn more about the effect of reaction rates on enzyme kinetics using the Michaelis Menten model. The value for the reaction from the enzyme-substrate complex going back into enzyme and substrate was adjusted, as was the constant for the reaction going from enzyme-substrate complex into product.
2. The Matlab programming came most easily to me.
3. The terminology section was the most difficult for me to understand. I got a little hung up on how to define a chemostat reactor and how to define the Lineweaver-Burk experiment.
4. I don't understand why we're using the Lineweaver-Burk plotting method for measuring enzyme kinetics. The Hanes-Woolf plot seems to be regarded as a superior method. Furthermore, the use of such plots has been made obsolete by nonlinear regression techniques; I'm sure that MatLab is capable of doing a nonlinear regression and giving us the parameters that we're looking for.

James C. Clements 16:56, 6 February 2011 (EST)

### Alondra Vega's Journal Entry

1. The purpose of this assignment wasn to see the different effects that the paramters can have in a function. Also, to give us practice with matlab and finish the introductuion of the Lineweaver-burke model.
2. The part of the assignment that came most easily to me was defining the terms. I feel that they are more mathematically based than biology based, so even if I did not know what they meant, it cool to learn about them. This section of the homework did not take me too long.
3. The most challenging part of this assignment was working with matlab and trying to figure out how to put all the plots in the same graph. I had never really worked in matlab and writing a code, so it was not very easy to navigate through the help menu. Once I figured that out, running the code was simple.
4. I still do not understand how the application comes in. If it were not for the legends in the graphs, I would not have been able to figure out what the figures represented. I feel that we are modeling concentrations, but I have a very strong feeling that i am wrong. I do not understand what we are running and why it is important to us. I also don't understand the difference between the catalysis driver and the Michaelis-Menten product driver; I feel that they give the same product.

Alondra Vega 17:44, 6 February 2011 (EST)