Team:KULeuven/Model/Output

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Revision as of 10:35, 14 August 2008

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Output

Position in the system

The output system is one of three modules directly linked to the output of the light sensor (black-box) the input for is OmpF. The output system is a simple gene regulation, of which transcription is activated by OmpF. The output signal is CFP (cyan fluorescent protein).

In the applied project of dealing with Crohn's disease this would be replaced by the drug necessary to cure the local inflammation. The drug concentration would be proportional to the amount of local inflammation sensed.

Describing the system

ODE's

Parameters

*Parameter values (Output)*
Name	Value	Comments	Reference
Degradation Rates
d_CFP (protein)	1.05E-4 s^-1		[http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link]
d_{RNA_CFP} (mRNA)	0.0023 s^-1		[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
Transcription Rates
k_CFP	OmpF dependent
Translation Rates
k_CFP	0.167 s^-1	RBS is B0032 (efficiency of 0.3)

Models

CellDesigner (SBML file)

Matlab (SBML file)

Simulations

Several simulations were conducted, the following two show the transient respons and eventual saturation of the output system to a low and a high step signal as input, respectively. We see that there is a great distinction in the number of CFP molecules between the two input signals.

Next figure shows the switching behaviour of the output system to an light signal turning off and on:

Sensitivity Analysis

@@ Line 66: / Line 66: @@
 === Models ===
 ==== CellDesigner ([https://static.igem.org/mediawiki/2008/5/53/Output_CellDesigner.zip SBML file]) ====
-The Output model represented in CellDesigner:
 [[Image:Output_CellDesigner.png|500px|center|Output]]
-Several simulations were conducted, the following two show the transient respons and eventual saturation of the output system to a low and a high step signal as input, respectively. We see that there is a great distinction in the number of CFP molecules between the two input signals.
-[[Image:Sim_output_1.png|780px|center]]
+==== Matlab ([https://static.igem.org/mediawiki/2008/1/16/Output_Matlab.zip SBML file]) ====
-[[Image:Sim_output_2.png|780px|center]]
-Next figure shows the switching behaviour of the output system to an light signal turning off and on:
-[[Image:Sim_output_3.png|780px|center]]
+[[Image:Output_Matlab.jpg|center]]
-==== Matlab ([https://static.igem.org/mediawiki/2008/1/16/Output_Matlab.zip SBML file]) ====
-The diagram for the output system is shown below:
+=== Simulations ===
-[[Image:Output_Matlab.jpg|center]]
+Several simulations were conducted, the following two show the transient respons and eventual saturation of the output system to a low and a high step signal as input, respectively. We see that there is a great distinction in the number of CFP molecules between the two input signals.
-Another two simulations have been conducted, matching the solutions found by CellDesigner, the low input respons (0.0005 OmpF s<sup>-1</sup>) is on the left, the high input respons (0.025 OmpF s<sup>-1</sup>) on the right:
+[[Image:Sim_output_1.png|780px|center]]
+[[Image:Sim_output_2.png|780px|center]]
-{| align="center"
+Next figure shows the switching behaviour of the output system to an light signal turning off and on:
-|[[Image:Sim_output_low_input.jpg|center|450px]]
-|[[Image:Sim_output_high_input.jpg|center|450px]]
-|}
-Next figure demonstrates the switching behaviour and concides with the results predicted by CellDesigner:
+[[Image:Sim_output_3.png|780px|center]]
-[[Image:Sim_output_switch_input.jpg|center]]
 === Sensitivity Analysis ===
 [[Image:Sens output2.png|center]]