BIOL398-03/S13:Class Journal Week 4 - Revision history

Salman Ahmad at 08:59, 8 February 2013

2013-02-08T08:59:05Z

←Older revision		Revision as of 08:59, 8 February 2013
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	===Reflection===		===Reflection===
	#What was the purpose of this assignment?		#What was the purpose of this assignment?
-	#*	+	#*Practice solving differential equations and deal with multiple variables.
	#What aspect of this assignment came most easily to you?		#What aspect of this assignment came most easily to you?
-	#*	+	#*The MATLAB part of the assignment was the easiest for me.
	#What aspect of this assignment was the most challenging for you?		#What aspect of this assignment was the most challenging for you?
-	#*	+	#*Doing all of the math.
	#What (yet) do you not understand?		#What (yet) do you not understand?
-	#*	+	#*I'm still not sure if I did my math right.

	===Read and Reflect===		===Read and Reflect===

	*Go back over the ter Schure paper. Which parameters in our model can you extract from the paper? Which must be found by some other methods? What steady states are provided in the paper?		*Go back over the ter Schure paper. Which parameters in our model can you extract from the paper? Which must be found by some other methods? What steady states are provided in the paper?
-	**	+	**The parameters from the paper were the ammonia concentration, carbon (glucose) concentration, and and the dilution. The only two rate constants that are not give to us are V and r.

	[[User:Salman Ahmad\|Salman Ahmad]] 00:14, 8 February 2013 (EST)		[[User:Salman Ahmad\|Salman Ahmad]] 00:14, 8 February 2013 (EST)

Elizabeth Polidan: Added one more comment.

2013-02-08T07:56:53Z

Added one more comment.

←Older revision		Revision as of 07:56, 8 February 2013
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	##Playing around with Matlab and understanding parameters and constants vs. state variables.		##Playing around with Matlab and understanding parameters and constants vs. state variables.
	#What aspect of this assignment was the most challenging for you?		#What aspect of this assignment was the most challenging for you?
-	##Remembering my algebra!	+	##Remembering my algebra! I sure hope some of that work is correct.
	#What (yet) do you not understand?		#What (yet) do you not understand?
	##Just waiting to see where we go from here.		##Just waiting to see where we go from here.

Matthew E. Jurek: answered the read and reflect

2013-02-08T07:35:06Z

answered the read and reflect

←Older revision		Revision as of 07:35, 8 February 2013
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	*What (yet) do you not understand?		*What (yet) do you not understand?
	**I still don't understand how to work through the steady state equations. I want to figure this out as I know we will continue to use these skills as the semester continues.		**I still don't understand how to work through the steady state equations. I want to figure this out as I know we will continue to use these skills as the semester continues.
		+	===Read and Reflect===
		+	*Go back over the ter Schure paper. Which parameters in our model can you extract from the paper? Which must be found by some other methods? What steady states are provided in the paper?
		+	**The ter Schure paper stated the dilution rate, the nitrogen feed rate, the carbon rate, and the glucose concentration. All of these are found in our model. The conversion rate and reaction rate must be found by some other method. The ammonia flux was kept steady in the paper.
		+	*'''[[User:Matthew E. Jurek\|Matthew E. Jurek]] 02:35, 8 February 2013 (EST)''':

Matthew E. Jurek: answered the last question

2013-02-08T07:27:28Z

answered the last question

←Older revision		Revision as of 07:27, 8 February 2013
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	*What was the purpose of this assignment?		*What was the purpose of this assignment?
	**The purpose of this assignment was to explore what we studied in the most recent journal club. This was done by expressing the chemostat in the experiment as a function on MatLab. Furthermore, this assignment required us to explore the math behind these functions.		**The purpose of this assignment was to explore what we studied in the most recent journal club. This was done by expressing the chemostat in the experiment as a function on MatLab. Furthermore, this assignment required us to explore the math behind these functions.
		+	*What aspect of this assignment came most easily to you?
		+	**Running the given script and manipulating the already established function. However, there was an error in the given script, but I was able to correct it and run it properly.
		+	*What aspect of this assignment was most challenging for you?
		+	**Working through the math. I haven't studied math in a while and this part was extremely difficult. I'm not sure what I did is correct, but I tried to work through as many variables as possible.
		+	*What (yet) do you not understand?
		+	**I still don't understand how to work through the steady state equations. I want to figure this out as I know we will continue to use these skills as the semester continues.

Matthew E. Jurek: /* =Questions */ fixed question header

2013-02-08T07:23:58Z

=Questions: fixed question header

←Older revision		Revision as of 07:23, 8 February 2013
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	==Matthew E. Jurek Week 4==		==Matthew E. Jurek Week 4==
	[[User:Matthew E. Jurek\|Matthew E. Jurek]]		[[User:Matthew E. Jurek\|Matthew E. Jurek]]
-	===Questions==	+	===Questions===
	*What was the purpose of this assignment?		*What was the purpose of this assignment?
	**The purpose of this assignment was to explore what we studied in the most recent journal club. This was done by expressing the chemostat in the experiment as a function on MatLab. Furthermore, this assignment required us to explore the math behind these functions.		**The purpose of this assignment was to explore what we studied in the most recent journal club. This was done by expressing the chemostat in the experiment as a function on MatLab. Furthermore, this assignment required us to explore the math behind these functions.

Matthew E. Jurek: answered first question

2013-02-08T07:23:31Z

answered first question

←Older revision		Revision as of 07:23, 8 February 2013
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	#*The paper provided the nitrogen concentration, carbon concentration, and dilution rate. The values of V, r, and K, which are the reaction maximum, the rate of conversion and reaction rate constant, respectively. The only steady state provided in the paper was ammonia concentration.		#*The paper provided the nitrogen concentration, carbon concentration, and dilution rate. The values of V, r, and K, which are the reaction maximum, the rate of conversion and reaction rate constant, respectively. The only steady state provided in the paper was ammonia concentration.
	[[User:Laura Terada\|Laura Terada]] 02:15, 8 February 2013 (EST)		[[User:Laura Terada\|Laura Terada]] 02:15, 8 February 2013 (EST)
		+
		+	==Matthew E. Jurek Week 4==
		+	[[User:Matthew E. Jurek\|Matthew E. Jurek]]
		+	===Questions==
		+	*What was the purpose of this assignment?
		+	**The purpose of this assignment was to explore what we studied in the most recent journal club. This was done by expressing the chemostat in the experiment as a function on MatLab. Furthermore, this assignment required us to explore the math behind these functions.

Laura Terada: laura terada submission

2013-02-08T07:15:06Z

laura terada submission

←Older revision		Revision as of 07:15, 8 February 2013
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	#*By looking at the Schure paper, the parameters that can be extracted are concerned with growth rate, carbon rate, and nitrogen feed. The paper emphasized that ammonia flux was constant. We will need to determine V and r.		#*By looking at the Schure paper, the parameters that can be extracted are concerned with growth rate, carbon rate, and nitrogen feed. The paper emphasized that ammonia flux was constant. We will need to determine V and r.
	[[User:Helena M. Olivieri\|Helena M. Olivieri]] 02:00, 8 February 2013 (EST)		[[User:Helena M. Olivieri\|Helena M. Olivieri]] 02:00, 8 February 2013 (EST)
		+
		+	==Laura Terada Week 4 Journal==
		+	[[User:Laura Terada\|Laura Terada]]
		+	===Questions===
		+	#What was the purpose of this assignment?
		+	#*The purpose of this assignment was for us to be able to mathematically understand the model of steady state conditions in terms of the yeast, carbon, and nitrogen state variables. It also tested our ability to do algebra.
		+	#What aspect of this assignment came most easily to you?
		+	#*Inserting the script and running the graph in MATLAB was the easiest.
		+	#What aspect of this assignment was the most challenging for you?
		+	#*Being able to derive the steady state for the state variables was the most challenging. After introducing the assignment in today's class, I was not comfortable deriving the equations. I worked on the equations for an extremely long time, and was still unable to fully complete the first question to the homework assignment.
		+	#What (yet) do you not understand?
		+	#*I still don't understand how to derive the steady state equations.
		+	===Read and Reflect===
		+	#Go back over the ter Schure paper. Which parameters in our model can you extract from the paper? Which must be found by some other methods? What steady states are provided in the paper?
		+	#*The paper provided the nitrogen concentration, carbon concentration, and dilution rate. The values of V, r, and K, which are the reaction maximum, the rate of conversion and reaction rate constant, respectively. The only steady state provided in the paper was ammonia concentration.
		+	[[User:Laura Terada\|Laura Terada]] 02:15, 8 February 2013 (EST)

Helena M. Olivieri: Undo revision 674608 by Helena M. Olivieri (Talk)

2013-02-08T07:00:55Z

Undo revision 674608 by Helena M. Olivieri (Talk)

←Older revision		Revision as of 07:00, 8 February 2013
Line 44:		Line 44:
	====Read and Reflect====		====Read and Reflect====
	*Go back over the ter Schure paper. Which parameters in our model can you extract from the paper? Which must be found by some other methods? What steady states are provided in the paper?		*Go back over the ter Schure paper. Which parameters in our model can you extract from the paper? Which must be found by some other methods? What steady states are provided in the paper?
-	**Both our work and the paper contain nutrient inflow rate, net growth rate (looking at biomass specifically), the nitrogen feed rate, and the carbon rate. However, in the paper, carbon rate was kept constant, but we treated it as a state variable. ~~The~~ The ammonia flux (steady state concentration of ammonia) was given in the paper.	+	**Both our work and the paper contain nutrient inflow rate, net growth rate (looking at biomass specifically), the nitrogen feed rate, and the carbon rate. However, in the paper, carbon rate was kept constant, but we treated it as a state variable. In reading the paper, we had to work to figure out all of the rate constants, the conversion factor, and the reaction maximum. The ammonia flux (steady state concentration of ammonia) was given in the paper, since all the data was assumed to be taken when the chemostat was at equilibrium.

		+	'''[[User:Kasey E. O'Connor\|Kasey E. O'Connor]] 01:43, 8 February 2013 (EST)'''

	==James P. McDonald Week 4 Journal==		==James P. McDonald Week 4 Journal==
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	[[User:Anthony J. Wavrin\|Anthony J. Wavrin]] 01:32, 8 February 2013 (EST)		[[User:Anthony J. Wavrin\|Anthony J. Wavrin]] 01:32, 8 February 2013 (EST)
		+
		+
		+	==Ashley Rhoades Week 4==
		+
		+	[[User: Ashley Rhoades \| Ashley Rhoades]]
		+
		+	===Reflection on Work===
		+	#What was the purpose of this assignment?
		+	#*The purpose of this assignment was to get more comfortable with differential equations in matlab and the chemostat models.
		+	#What aspect of this assignment came most easily to you?
		+	#*Running the functions in matlab was easy.
		+	#What aspect of this assignment was the most challenging for you?
		+	#*It was difficult keeping track of all the parameters in the mathematics of this assignment
		+	#What (yet) do you not understand?
		+	#*I probably couldn't put those functions into matlab very easily. There is a lot of formatting that we learned that still hasn't stuck with me.
		+
		+	===Read and Reflect===
		+
		+	*Go back over the ter Schure paper. Which parameters in our model can you extract from the paper? Which must be found by some other methods? What steady states are provided in the paper?
		+	**Parameters that were extracted from the paper were the dilution rate, the nitrogen feed, and the carbon feed. What had to be found through other methods were the net growth, nutrient consumption, and nutrient saturation. The paper does not go to steady state values. The experiments stop before the steady states are reached.
		+
		+	[[User:Ashley Rhoades\|Ashley Rhoades]] 01:48, 8 February 2013 (EST)
		+
		+	==Elizabeth Polidan Class Journal Week 4==
		+	[[User:Elizabeth Polidan\|Elizabeth Polidan]]
		+
		+	===Reflection on Work===
		+	#What was the purpose of this assignment?
		+	##To help us understand how these mathematical equations create information we can analyze and assess.
		+	##To help us understand the ideas of parameters and constants and get us used to using them.
		+	##To give us practice using Matlab.
		+	#What aspect of this assignment came most easily to you?
		+	##Playing around with Matlab and understanding parameters and constants vs. state variables.
		+	#What aspect of this assignment was the most challenging for you?
		+	##Remembering my algebra!
		+	#What (yet) do you not understand?
		+	##Just waiting to see where we go from here.
		+
		+	[[User:Elizabeth Polidan\|Elizabeth Polidan]] 01:51, 8 February 2013 (EST)

	==Helena M. Olivieri Week 4 Journal==		==Helena M. Olivieri Week 4 Journal==
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	#Go back over the ter Schure paper. Which parameters in our model can you extract from the paper? Which must be found by some other methods? What steady states are provided in the paper?		#Go back over the ter Schure paper. Which parameters in our model can you extract from the paper? Which must be found by some other methods? What steady states are provided in the paper?
	#*By looking at the Schure paper, the parameters that can be extracted are concerned with growth rate, carbon rate, and nitrogen feed. The paper emphasized that ammonia flux was constant. We will need to determine V and r.		#*By looking at the Schure paper, the parameters that can be extracted are concerned with growth rate, carbon rate, and nitrogen feed. The paper emphasized that ammonia flux was constant. We will need to determine V and r.
-	[[User:Helena M. Olivieri\|Helena M. Olivieri]] 01:54, 8 February 2013 (EST)	+	[[User:Helena M. Olivieri\|Helena M. Olivieri]] 02:00, 8 February 2013 (EST)

Helena M. Olivieri at 06:54, 8 February 2013

2013-02-08T06:54:37Z

←Older revision		Revision as of 06:54, 8 February 2013
Line 44:		Line 44:
	====Read and Reflect====		====Read and Reflect====
	*Go back over the ter Schure paper. Which parameters in our model can you extract from the paper? Which must be found by some other methods? What steady states are provided in the paper?		*Go back over the ter Schure paper. Which parameters in our model can you extract from the paper? Which must be found by some other methods? What steady states are provided in the paper?
-	**Both our work and the paper contain nutrient inflow rate, net growth rate (looking at biomass specifically), the nitrogen feed rate, and the carbon rate. However, in the paper, carbon rate was kept constant, but we treated it as a state variable. ~~In reading the paper, we had to work to figure out all of the rate constants, the conversion factor, and the reaction maximum.~~ The ammonia flux (steady state concentration of ammonia) was given in the paper~~, since all the data was assumed to be taken when the chemostat was at equilibrium~~.	+	**Both our work and the paper contain nutrient inflow rate, net growth rate (looking at biomass specifically), the nitrogen feed rate, and the carbon rate. However, in the paper, carbon rate was kept constant, but we treated it as a state variable. The The ammonia flux (steady state concentration of ammonia) was given in the paper.

-	~~'''[[User:Kasey E. O'Connor\|Kasey E. O'Connor]] 01:43, 8 February 2013 (EST)'''~~

	==James P. McDonald Week 4 Journal==		==James P. McDonald Week 4 Journal==
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	[[User:Anthony J. Wavrin\|Anthony J. Wavrin]] 01:32, 8 February 2013 (EST)		[[User:Anthony J. Wavrin\|Anthony J. Wavrin]] 01:32, 8 February 2013 (EST)

-		+	==Helena M. Olivieri Week 4 Journal==
-	==~~Ashley Rhoades~~ Week 4==	+	[[User:Helena M. Olivieri\|Helena M. Olivieri]]
-		+	===Questions===
-	[[User: ~~Ashley Rhoades~~ \| ~~Ashley Rhoades~~]]	+
-		+
-	===~~Reflection on Work~~===	+
	#What was the purpose of this assignment?		#What was the purpose of this assignment?
-	#*The purpose ~~of this assignment~~ was to ~~get more comfortable with differential equations in matlab~~ and the ~~chemostat models~~.	+	#*The purpose was to further delve into the functions of Matlab, as well as to fully understand the algebraic functions and derivatives behind the Matlab inputs.
	#What aspect of this assignment came most easily to you?		#What aspect of this assignment came most easily to you?
-	#*~~Running the functions in~~ matlab was ~~easy~~.	+	#*The matlab aspect was the easiest because the most difficult part, the code writing, was already done.
	#What aspect of this assignment was the most challenging for you?		#What aspect of this assignment was the most challenging for you?
-	#*It was ~~difficult keeping track of all the parameters in the mathematics of this assignment~~	+	#*The algebra was slightly less than pleasant.
-	#What (yet) do you not understand?	+	#What (yet) do you not understand?
-	#*~~I probably couldn't put those functions into matlab very easily~~. ~~There is a lot of formatting that we learned that still hasn't stuck with me~~.	+	#*How to develop the codes in Matlab... as well as how to make algebra pleasant (haha).

	===Read and Reflect===		===Read and Reflect===
-		+	#Go back over the ter Schure paper. Which parameters in our model can you extract from the paper? Which must be found by some other methods? What steady states are provided in the paper?
-	*Go back over the ter Schure paper. Which parameters in our model can you extract from the paper? Which must be found by some other methods? What steady states are provided in the paper?	+	#*By looking at the Schure paper, the parameters that can be extracted are concerned with growth rate, carbon rate, and nitrogen feed. The paper emphasized that ammonia flux was constant. We will need to determine V and r.
-	**Parameters that were extracted from the paper ~~were the dilution rate~~, the ~~nitrogen feed, and the carbon feed. What had to~~ be ~~found through other methods were the net~~ growth, ~~nutrient consumption~~, and ~~nutrient saturation~~. The paper ~~does not go to steady state values. The experiments stop before the steady states are reached.~~	+	[[User:Helena M. Olivieri\|Helena M. Olivieri]] 01:54, 8 February 2013 (EST)
-		+
-	~~[[User:Ashley Rhoades\|Ashley Rhoades]] 01:48, 8 February 2013 (EST)~~	+
-		+
-	~~==Elizabeth Polidan Class Journal Week 4==~~	+
-	~~[[User:Elizabeth Polidan\|Elizabeth Polidan]]~~	+
-		+
-	~~===Reflection on Work===~~	+
-	~~#What~~ was ~~the purpose of this assignment?~~	+
-	~~##To help us understand how these mathematical equations create information we can analyze and assess~~.	+
-	~~##To help us understand the ideas of parameters and constants and get us used~~ to ~~using them.~~	+
-	~~##To give us practice using Matlab.~~	+
-	~~#What aspect of this assignment came most easily to you?~~	+
-	~~##Playing around with Matlab and understanding parameters~~ and ~~constants vs. state variables~~.	+
-	~~#What aspect of this assignment was the most challenging for you?~~	+
-	~~##Remembering my algebra!~~	+
-	~~#What (yet) do you not understand?~~	+
-	~~##Just waiting to see where we go from here.~~	+
-		+
-	[[User:~~Elizabeth Polidan~~\|~~Elizabeth Polidan~~]] 01:51, 8 February 2013 (EST)	+

Elizabeth Polidan: Added my responses

2013-02-08T06:51:25Z

Added my responses

←Older revision		Revision as of 06:51, 8 February 2013
Line 129:		Line 129:

	[[User:Ashley Rhoades\|Ashley Rhoades]] 01:48, 8 February 2013 (EST)		[[User:Ashley Rhoades\|Ashley Rhoades]] 01:48, 8 February 2013 (EST)
		+
		+	==Elizabeth Polidan Class Journal Week 4==
		+	[[User:Elizabeth Polidan\|Elizabeth Polidan]]
		+
		+	===Reflection on Work===
		+	#What was the purpose of this assignment?
		+	##To help us understand how these mathematical equations create information we can analyze and assess.
		+	##To help us understand the ideas of parameters and constants and get us used to using them.
		+	##To give us practice using Matlab.
		+	#What aspect of this assignment came most easily to you?
		+	##Playing around with Matlab and understanding parameters and constants vs. state variables.
		+	#What aspect of this assignment was the most challenging for you?
		+	##Remembering my algebra!
		+	#What (yet) do you not understand?
		+	##Just waiting to see where we go from here.
		+
		+	[[User:Elizabeth Polidan\|Elizabeth Polidan]] 01:51, 8 February 2013 (EST)