IGEM:IMPERIAL/2008/New/Growth Curve - Revision history

Prudence Wing-Yan Wong at 12:50, 25 October 2008

Prudence Wing-Yan Wong — Sat, 25 Oct 2008 12:50:46 GMT

←Older revision		Revision as of 12:50, 25 October 2008
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	*Time span of lag phase, stationary phase and exponential phase		*Time span of lag phase, stationary phase and exponential phase
	*The growth rate}}		*The growth rate}}
		+
		+
		+	{{Imperial/Box1\|The Model\|
		+	The model illustrates the main growth phases the ''B. subtilis'' undergoes. These are identified as the '''lag phase''', the '''exponential phase''' and the '''stationary phase'''. The death phase is a constitutive event and it is possible that it exerts an influence on the three phases discussed below. However, to simplify a complicated model, it is less relevant in this case and therefore is not included in this model.
		+
		+	The M-file used to generate the model below is located in the Appendices section of the Dry Lab hub.
		+
		+	<center>[[Image:Nutrient ft.TIF\|500px]][[Image:Label_model.TIF‎\|500px]]</center>}}
		+

	{{Imperial/Box1\|Results\|		{{Imperial/Box1\|Results\|
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	}}		}}

-	~~{{Imperial/Box1\|The Model\|~~
-	The model illustrates the main growth phases the ''B. subtilis'' undergoes. These are identified as the '''lag phase''', the '''exponential phase''' and the '''stationary phase'''. The death phase is a constitutive event and it is possible that it exerts an influence on the three phases discussed below. However, to simplify a complicated model, it is less relevant in this case and therefore is not included in this model.

-	~~The M-file used to generate the model below is located in the Appendices section of the Dry Lab hub.~~
-
-	~~<center>[[Image:Nutrient ft.TIF\|500px]][[Image:Label_model.TIF‎\|500px]]</center>}}~~

	{{Imperial/EndPage\|Dry_Lab\|Genetic_Circuit}}		{{Imperial/EndPage\|Dry_Lab\|Genetic_Circuit}}

Qin Qi: Undo revision 248026 by Qin Qi (Talk)

Qin Qi — Wed, 01 Oct 2008 14:55:42 GMT

Undo revision 248026 by Qin Qi (Talk)

←Older revision		Revision as of 14:55, 1 October 2008
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	The M-file used to generate the model below is located in the Appendices section of the Dry Lab hub.		The M-file used to generate the model below is located in the Appendices section of the Dry Lab hub.

-	<center>[[Image:Nutrient ft.TIF\|500px]]~~</center>~~	+	<center>[[Image:Nutrient ft.TIF\|500px]][[Image:Label_model.TIF‎\|500px]]</center>}}
-	~~<center>~~[[Image:Label_model.TIF‎\|500px]]</center>}}	+

	{{Imperial/EndPage\|Dry_Lab\|Genetic_Circuit}}		{{Imperial/EndPage\|Dry_Lab\|Genetic_Circuit}}

Qin Qi at 14:51, 1 October 2008

Qin Qi — Wed, 01 Oct 2008 14:51:02 GMT

←Older revision		Revision as of 14:51, 1 October 2008
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	The M-file used to generate the model below is located in the Appendices section of the Dry Lab hub.		The M-file used to generate the model below is located in the Appendices section of the Dry Lab hub.

-	<center>[[Image:Nutrient ft.TIF\|500px]][[Image:Label_model.TIF‎\|500px]]</center>}}	+	<center>[[Image:Nutrient ft.TIF\|500px]]</center>
		+	<center>[[Image:Label_model.TIF‎\|500px]]</center>}}

	{{Imperial/EndPage\|Dry_Lab\|Genetic_Circuit}}		{{Imperial/EndPage\|Dry_Lab\|Genetic_Circuit}}

Qin Qi: Undo revision 248019 by Qin Qi (Talk)

Qin Qi — Wed, 01 Oct 2008 13:02:04 GMT

Undo revision 248019 by Qin Qi (Talk)

←Older revision		Revision as of 13:02, 1 October 2008
Line 64:		Line 64:

	The M-file used to generate the model below is located in the Appendices section of the Dry Lab hub.		The M-file used to generate the model below is located in the Appendices section of the Dry Lab hub.
-	~~<html><table border="0" cellpadding="5" cellspacing="0" align="center"><tr><td width=50%></html>~~	+
-	<center>[[Image:Nutrient ft.TIF]]	+	<center>[[Image:Nutrient ft.TIF\|500px]][[Image:Label_model.TIF‎\|500px]]</center>}}
-	[[Image:Label_model.TIF‎]]</center>}}	+

	{{Imperial/EndPage\|Dry_Lab\|Genetic_Circuit}}		{{Imperial/EndPage\|Dry_Lab\|Genetic_Circuit}}

Qin Qi at 13:01, 1 October 2008

Qin Qi — Wed, 01 Oct 2008 13:01:42 GMT

←Older revision		Revision as of 13:01, 1 October 2008
Line 64:		Line 64:

	The M-file used to generate the model below is located in the Appendices section of the Dry Lab hub.		The M-file used to generate the model below is located in the Appendices section of the Dry Lab hub.
-		+	<html><table border="0" cellpadding="5" cellspacing="0" align="center"><tr><td width=50%></html>
-	<center>[[Image:Nutrient ft.TIF~~\|500px~~]][[Image:Label_model.TIF‎~~\|500px~~]]</center>}}	+	<center>[[Image:Nutrient ft.TIF]]
		+	[[Image:Label_model.TIF‎]]</center>}}

	{{Imperial/EndPage\|Dry_Lab\|Genetic_Circuit}}		{{Imperial/EndPage\|Dry_Lab\|Genetic_Circuit}}

Qin Qi at 13:00, 1 October 2008

Qin Qi — Wed, 01 Oct 2008 13:00:35 GMT

←Older revision		Revision as of 13:00, 1 October 2008
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	{{Imperial/Box1\|Results\|		{{Imperial/Box1\|Results\|
	The model for the growth curve was fitted to the experimental results as shown below. The experimental results is depicted by the red curve, while our model is shown by the green curve. The resource curve was also plotted as a function of time and is shown below. Based on our experimental results from the Wet Lab, a log graph was plotted to determine the growth rate. The growth rate was then determined from the gradient of the log graph. This value was included when simulating the growth model using MATLAB.		The model for the growth curve was fitted to the experimental results as shown below. The experimental results is depicted by the red curve, while our model is shown by the green curve. The resource curve was also plotted as a function of time and is shown below. Based on our experimental results from the Wet Lab, a log graph was plotted to determine the growth rate. The growth rate was then determined from the gradient of the log graph. This value was included when simulating the growth model using MATLAB.
-	<html><table border="0" cellpadding="5" cellspacing="0" align="center"><tr><td></html>[[Image:Experimental_Result.JPG\|thumb\|center~~\|300px~~]]<html>	+	<html><table border="0" cellpadding="5" cellspacing="0" align="center"><tr><td width=33%></html>[[Image:Experimental_Result.JPG\|thumb\|center]]<html>
-	</td><td></html>[[Image:Fitted_Curve.JPG‎\|thumb\|center~~\|300px~~]]<html>	+	</td><td></html>[[Image:Fitted_Curve.JPG‎\|thumb\|center]]<html>
-	</td><td></html>[[Image:Resource_Curve.JPG‎\|thumb\|center~~\|300px~~]]<html>	+	</td><td></html>[[Image:Resource_Curve.JPG‎\|thumb\|center]]<html>
	</td></tr><tr><td><center>Experimental Results</center>		</td></tr><tr><td><center>Experimental Results</center>
	</td><td><center>Fitted Curve</center>		</td><td><center>Fitted Curve</center>

Tom Adie at 11:48, 30 September 2008

Tom Adie — Tue, 30 Sep 2008 11:48:25 GMT

←Older revision		Revision as of 11:48, 30 September 2008
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	<br>		<br>
	<br>		<br>
-	{{Imperial/~~Box1~~\|Growth Curve\|	+	{{Imperial/Box2\|Growth Curve\|
	Part of our dry lab team concentrated on modelling the growth curve of ''B. subtilis''. This is important to characterise the chassis; particularly, the growth of ''subtilis'' is a vital parameter for planning experiments for future projects. Characterisation increases the predictability of the growth of B. subtilis by determining, for example, its growth rate and the duration of its distinctive growth phases. In order to model the growth of ''B. subtilis'', the process was broken down into three main steps, where a separate submodel is produced in MATLAB for each step. Each submodel is an ODE model, which can be simulated using MATLAB. The variables in each submodel can be adjusted according to the boundary conditions (from experimental results).		Part of our dry lab team concentrated on modelling the growth curve of ''B. subtilis''. This is important to characterise the chassis; particularly, the growth of ''subtilis'' is a vital parameter for planning experiments for future projects. Characterisation increases the predictability of the growth of B. subtilis by determining, for example, its growth rate and the duration of its distinctive growth phases. In order to model the growth of ''B. subtilis'', the process was broken down into three main steps, where a separate submodel is produced in MATLAB for each step. Each submodel is an ODE model, which can be simulated using MATLAB. The variables in each submodel can be adjusted according to the boundary conditions (from experimental results).

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	\|[[Image:Log_graph.tif\|300px\|Log-Graph used to determine the growth rate]]}}		\|[[Image:Log_graph.tif\|300px\|Log-Graph used to determine the growth rate]]}}

-	{{Imperial/~~Box2~~\|Key Phases of Bacterial Growth\|	+	{{Imperial/Box1\|Key Phases of Bacterial Growth\|
	===Lag Phase===		===Lag Phase===
	During the lag phase, the rate of growth is slow due to two main reasons, ''B. subtilis'' is absorbing nutrients in the medium and the replication machinery is being switched on. The higher the concentration of nutrients in the medium, the faster the rate of bateria growth.		During the lag phase, the rate of growth is slow due to two main reasons, ''B. subtilis'' is absorbing nutrients in the medium and the replication machinery is being switched on. The higher the concentration of nutrients in the medium, the faster the rate of bateria growth.

Tom Adie at 11:48, 30 September 2008

Tom Adie — Tue, 30 Sep 2008 11:48:09 GMT

←Older revision		Revision as of 11:48, 30 September 2008
Line 3:		Line 3:
	<br>		<br>
	<br>		<br>
-	{{Imperial/~~Box2~~\|Growth Curve\|	+	{{Imperial/Box1\|Growth Curve\|
	Part of our dry lab team concentrated on modelling the growth curve of ''B. subtilis''. This is important to characterise the chassis; particularly, the growth of ''subtilis'' is a vital parameter for planning experiments for future projects. Characterisation increases the predictability of the growth of B. subtilis by determining, for example, its growth rate and the duration of its distinctive growth phases. In order to model the growth of ''B. subtilis'', the process was broken down into three main steps, where a separate submodel is produced in MATLAB for each step. Each submodel is an ODE model, which can be simulated using MATLAB. The variables in each submodel can be adjusted according to the boundary conditions (from experimental results).		Part of our dry lab team concentrated on modelling the growth curve of ''B. subtilis''. This is important to characterise the chassis; particularly, the growth of ''subtilis'' is a vital parameter for planning experiments for future projects. Characterisation increases the predictability of the growth of B. subtilis by determining, for example, its growth rate and the duration of its distinctive growth phases. In order to model the growth of ''B. subtilis'', the process was broken down into three main steps, where a separate submodel is produced in MATLAB for each step. Each submodel is an ODE model, which can be simulated using MATLAB. The variables in each submodel can be adjusted according to the boundary conditions (from experimental results).

Tom Adie at 11:47, 30 September 2008

Tom Adie — Tue, 30 Sep 2008 11:47:53 GMT

←Older revision		Revision as of 11:47, 30 September 2008
Line 15:		Line 15:
	The graph on the right shows the log graph used to determine the growth rate.		The graph on the right shows the log graph used to determine the growth rate.
	\|[[Image:Log_graph.tif\|300px\|Log-Graph used to determine the growth rate]]}}		\|[[Image:Log_graph.tif\|300px\|Log-Graph used to determine the growth rate]]}}
		+
		+	{{Imperial/Box2\|Key Phases of Bacterial Growth\|
		+	===Lag Phase===
		+	During the lag phase, the rate of growth is slow due to two main reasons, ''B. subtilis'' is absorbing nutrients in the medium and the replication machinery is being switched on. The higher the concentration of nutrients in the medium, the faster the rate of bateria growth.
		+
		+	As a result, the volume of the bacteria increases, followed by an increase in the number of bacteria.
		+
		+	=== Exponential Phase ===
		+	Both colony number and cell volume increase exponentially during this phase. Our model assumes concentration of the nutrients inside the bacteria is constant.
		+
		+	=== Stationary Phase ===
		+	The growth of the colony ceases in number and in volume due to a finite concentration of nutrients, hence it does not have a gradient. Other causes may be death and cell division.
		+
		+	According to the model, the maximum growth of the bacteria is determined by the concentration of nutrients available initially.
		+
		+	To further enhance the accuracy of the model, the following information will be extracted from experimental data:
		+
		+	*Time span of lag phase, stationary phase and exponential phase
		+	*The growth rate}}

	{{Imperial/Box1\|Results\|		{{Imperial/Box1\|Results\|
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	The model illustrates the main growth phases the ''B. subtilis'' undergoes. These are identified as the '''lag phase''', the '''exponential phase''' and the '''stationary phase'''. The death phase is a constitutive event and it is possible that it exerts an influence on the three phases discussed below. However, to simplify a complicated model, it is less relevant in this case and therefore is not included in this model.		The model illustrates the main growth phases the ''B. subtilis'' undergoes. These are identified as the '''lag phase''', the '''exponential phase''' and the '''stationary phase'''. The death phase is a constitutive event and it is possible that it exerts an influence on the three phases discussed below. However, to simplify a complicated model, it is less relevant in this case and therefore is not included in this model.

-	The M-file used to generate the model below is located in the Appendices section~~, its link can be found at the bottom~~ of ~~this page~~.	+	The M-file used to generate the model below is located in the Appendices section of the Dry Lab hub.

-	[[Image:Nutrient ft.TIF\|500px~~\|center~~]]	+	<center>[[Image:Nutrient ft.TIF\|500px]][[Image:Label_model.TIF‎\|500px]]</center>}}
-	[[Image:Label_model.TIF‎\|500px~~\|center~~]]	+
-		+
-	~~==Key Phases of Bacterial Growth==~~	+
-		+
-		+
-	~~===LAG PHASE ===~~	+
-		+
-		+
-	During the lag phase, the rate of growth is slow due to two main reasons, ''B. subtilis'' is absorbing nutrients in the medium and the replication machinery is being switched on. The higher the concentration of nutrients in the medium, the faster the rate of bateria growth.	+
-		+
-	~~As a result, the volume of the bacteria increases, followed by an increase in the number of bacteria.~~	+
-		+
-	~~=== EXPONENTIAL PHASE ===~~	+
-		+
-		+
-	~~Both colony number and cell volume increase exponentially during this phase. Our model assumes concentration of the nutrients inside the bacteria is constant.~~	+
-		+
-	~~=== STATIONARY PHASE ===~~	+
-		+
-		+
-	~~The growth of the colony ceases in number and in volume due to a finite concentration of nutrients, hence it does not have a gradient. Other causes may be death and cell division.~~	+
-		+
-	~~According to the model, the maximum growth of the bacteria is determined by the concentration of nutrients available initially.~~	+
-		+
-	~~To further enhance the accuracy of the model, the following information will be extracted from experimental data:~~	+
-		+
-	*Time span of lag phase, stationary phase and exponential phase	+
-	*The growth rate}}	+
-		+
-	~~{{Imperial~~/~~Box1\|\|~~	+
-	~~==Discussion==~~	+
-		+
-	~~[[IGEM:IMPERIAL/2008/New/Dry_lab \| Dry lab hub]]~~	+
-		+
-	~~Growth Curve~~	+
-		+
-	~~[[IGEM:IMPERIAL/2008/New/Genetic_Circuit \| Genetic Circuit]]~~	+
-		+
-	~~[[IGEM:IMPERIAL/2008/New/Motility \| Motility]]~~	+
-		+
-	~~[[IGEM:IMPERIAL/2008/New/Appendices \| Appendices]]~~	+
-	}}	+

	{{Imperial/EndPage\|Dry_Lab\|Genetic_Circuit}}		{{Imperial/EndPage\|Dry_Lab\|Genetic_Circuit}}

Tom Adie at 11:40, 30 September 2008

Tom Adie — Tue, 30 Sep 2008 11:40:42 GMT

←Older revision		Revision as of 11:40, 30 September 2008
Line 4:		Line 4:
	<br>		<br>
	{{Imperial/Box2\|Growth Curve\|		{{Imperial/Box2\|Growth Curve\|
-	Part of our dry lab team concentrated on modelling the growth curve of ''B. subtilis''. This is important to characterise the chassis; particularly, the growth of ''subtilis'' is a vital parameter for planning experiments for future projects.	+	Part of our dry lab team concentrated on modelling the growth curve of ''B. subtilis''. This is important to characterise the chassis; particularly, the growth of ''subtilis'' is a vital parameter for planning experiments for future projects. Characterisation increases the predictability of the growth of B. subtilis by determining, for example, its growth rate and the duration of its distinctive growth phases. In order to model the growth of ''B. subtilis'', the process was broken down into three main steps, where a separate submodel is produced in MATLAB for each step. Each submodel is an ODE model, which can be simulated using MATLAB. The variables in each submodel can be adjusted according to the boundary conditions (from experimental results).
		+
		+	In the final step, a combination of Submodels 1 and 2 are superposed with Submodel 3, resulting in a more complex model which enhances the accuracy of illustrating bacterial growth. For more details about the submodels, please click on the following links:
		+
		+
		+	'''[[Tutorial for Growth Curve]]''' (More details about each submodel)
		+
		+	'''[[Media:Modelling_Growth_Curve.pdf]]''' (The tutorial questions)

	The graph on the right shows the log graph used to determine the growth rate.		The graph on the right shows the log graph used to determine the growth rate.
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	}}		}}

-	~~<br><br>~~	+	{{Imperial/Box1\|The Model\|
		+	The model illustrates the main growth phases the ''B. subtilis'' undergoes. These are identified as the '''lag phase''', the '''exponential phase''' and the '''stationary phase'''. The death phase is a constitutive event and it is possible that it exerts an influence on the three phases discussed below. However, to simplify a complicated model, it is less relevant in this case and therefore is not included in this model.

-	~~==Background Information of Modelling the Growth Curve==~~
-	{{Imperial/Box1\|\|The aim of modelling the growth curve is to characterise the ''B. subtilis'' chassis used in the project. Characterisation increases the predictability of the growth of '' B. subtilis'' by determining, for example, its growth rate and the duration of its distinctive growth phases.
-
-
-	~~===How to model the growth curve?===~~
-
-	In order to model the growth of ''B. subtilis'', the process was broken down into three main steps, where a separate submodel is produced in MATLAB for each step. Each submodel is an ODE model, which can be simulated using MATLAB. The variables in each submodel can be adjusted according to the boundary conditions (from experimental results).
-
-	In the final step, a combination of Submodels 1 and 2 are superposed with Submodel 3, resulting in a more complex model which enhances the accuracy of illustrating bacterial growth. For more details about the submodels, please click on the following links:
-
-
-	~~'''[[Tutorial for Growth Curve]]''' (More details about each submodel)~~
-
-	~~'''[[Media:Modelling_Growth_Curve.pdf]]''' (The tutorial questions)~~
-
-	~~===The Model===~~
-
-
-	The model illustrates the main growth phases the ''B. subtilis'' undergoes. These are identified as the '''lag phase''', the '''exponential phase''' and the '''stationary phase'''. The death phase is a constitutive event and it is possible that it exerts an influence on the three phases discussed below. However, to simplify a complicated model, it is less relevant in this case and therefore is not included in this model.
	The M-file used to generate the model below is located in the Appendices section, its link can be found at the bottom of this page.		The M-file used to generate the model below is located in the Appendices section, its link can be found at the bottom of this page.

Line 85:		Line 74:

	*Time span of lag phase, stationary phase and exponential phase		*Time span of lag phase, stationary phase and exponential phase
-	*The growth rate	+	*The growth rate}}
-		+
-		+
-	}}	+
-		+
-		+
-		+
-		+

	{{Imperial/Box1\|\|		{{Imperial/Box1\|\|