Difference between revisions of "IGEM:Imperial/2010/Modelling"

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{{Imperial2010/Header}}
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== Menu ==
 
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<div class="accordionButton"><b>Overview</b></div>
 
<div class="accordionButton"><b>Overview</b></div>
<div class="accordionContent",><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Overview"><b>Here is a a short overview of the two models.</b></a><br /><br /></div>
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<div class="accordionContent",><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Overview"><b>Here is a short overview of the two models.</b></a><br /><br /></div>
 
 
 
<div class="accordionButton"><b>Output Amplification Model</b></div>
 
<div class="accordionButton"><b>Output Amplification Model</b></div>
<div class="accordionContent"><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Michaelis_Menten"><b>Model based on Michaelis Menten Kinetics</b></a><br />Comparison between different amplification models (HIV1 and TEV) based on Michaelis Menten kinetics. However, Michaelis Menten kinetics does not apply to our system. Therefore, it had to be modelled from first principle (see below using law of mass action).<br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Michaelis_Menten#HIV1"><img src="http://www.openwetware.org/images/0/03/Slide2.JPG" height="150" width="200" alt="Model using HIV1"/></a> <a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Michaelis_Menten#TEV"><img src="http://www.openwetware.org/images/4/48/TEV.jpg" height="150" width="200" alt="Model using TEV"/></a><br /><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Mass_Action"><b>Model based on Law of Mass Action</b></a><br />Comparison between these 3 different models: Simple production, 1-step and 2-step amplification.<br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Mass_Action#Model_preA:_Simple_Production_of_Dioxygenase"><img src="http://www.openwetware.org/images/7/7f/Simple_production.JPG" height="100" width="300" alt="Simple Production"/></a> <a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Mass_Action#Model_A:_Activation_of_Dioxygenase_by_TEV_enzyme"><img src="http://www.openwetware.org/images/1/1c/1-step_amplification.JPG" height="100" width="300" alt="1-step amplification"/></a> <a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Mass_Action#Model_B:_Activation_of_Dioxygenase_by_TEV_or_activated_split_TEV_enzyme"><img src="http://www.openwetware.org/images/0/02/2-step_amplification.JPG" height="100" width="300" alt="2-step amplification"/></a><br /><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Variables1"><b>Variables and Constants</b></a><br />Here are the variables and constants that are used in the Protein Display Model.<br /><br /></div>
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<div class="accordionContent"><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Michaelis_Menten"><b>Model based on Michaelis Menten Kinetics</b></a><br />Comparison between different amplification models (HIV1 and TEV) based on Michaelis Menten kinetics. However, Michaelis Menten kinetics does not apply to our system. Therefore, it had to be modelled from first principle (see below using law of mass action).<br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Michaelis_Menten#HIV1"><img src="http://www.openwetware.org/images/0/03/Slide2.JPG" height="150" width="200" alt="Model using HIV1"/></a> <a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Michaelis_Menten#TEV"><img src="http://www.openwetware.org/images/4/48/TEV.jpg" height="150" width="200" alt="Model using TEV"/></a><br /><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Mass_Action"><b>Model based on Law of Mass Action</b></a><br />Comparison between these 3 different models: Simple production, 1-step and 2-step amplification.<br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Mass_Action#Model_preA:_Simple_Production_of_Dioxygenase"><img src="http://www.openwetware.org/images/7/7f/Simple_production.JPG" height="100" width="300" alt="Simple Production"/></a> <a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Mass_Action#Model_A:_Activation_of_Dioxygenase_by_TEV_enzyme"><img src="http://www.openwetware.org/images/1/1c/1-step_amplification.JPG" height="100" width="300" alt="1-step amplification"/></a> <a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Mass_Action#Model_B:_Activation_of_Dioxygenase_by_TEV_or_activated_split_TEV_enzyme"><img src="http://www.openwetware.org/images/0/02/2-step_amplification.JPG" height="100" width="300" alt="2-step amplification"/></a><br /><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Variables1"><b>Variables and Constants</b></a><br />Here are the variables and constants that are used in the Output Amplification Model.<br /><br /></div>
 
 
 
<div class="accordionButton"><b>Protein Display Model</b></div>
 
<div class="accordionButton"><b>Protein Display Model</b></div>
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<div class="accordionContent"><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Experiments1"><b>Experiments for the Output Amplification Model</b></a><br /><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Experiments2"><b>Experiments for the Protein Display Model</b></a><br /><br /></div>
 
<div class="accordionContent"><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Experiments1"><b>Experiments for the Output Amplification Model</b></a><br /><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Experiments2"><b>Experiments for the Protein Display Model</b></a><br /><br /></div>
 
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<br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/>
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==Engineering approach to project==
 +
[[Image:Engineering_cycle.jpg|500px|thumb|center]]
 +
1. Influence of Specification on Design and vice versa:
 +
*It was one of the longest steps as we were struggling to compromise the specifications with the viable designs.
 +
2. Influence of Design on Modelling and vice versa:
 +
*All modelling done was meant to give answers to questions that arose in the design phase.
 +
*Once designs were chosen, they were modelled. It was found that 2 step amplification is not likely to be effiecient, so it was decided that only 1step amplification will be taken forward to assembly. This was a significant conclusion as it would take weeks in the labroatory to find that out.
 +
*The doubt about big enough gradient of AIPs to be established in the extracellular space to set off receptor was rationalised by modelling. The model allowed to determine conditions for the system to work
 +
3. Influence of Modelling on Assembly and vice versa:
 +
*The results from modelling allowed to progress with assembly
 +
4. Influence of Assembly on Testing and vice versa:
 +
*testing has been planned ahead, so assembly contructs have been modified to allow some testing methods like: purification or negative control.
 +
5. Influence of Testing on Specifications and vice versa:
 +
*We did not get there yet. However, if the specifications would not be met by the results, we would need to try redesigning the system or, in case of no alternative, changing the specifications.
 +
6. Influence of components not adjacent to each other in the cycle:
 +
*Testing may influence modelling as the results of the two do not match.
 +
*Many experiments were diesgned specifically on the request of modellers in order to find parameters for the models. Obtaining those paramters would increase the reliability of the models.

Latest revision as of 13:58, 12 October 2010

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} </style> </head> <body style="background-color:FFFFCC"> <div id="wrapper"> <div class="accordionButton"><b>Objectives</b></div> <div class="accordionContent",><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Objectives"><b>Here are our daily objectives.</b></a><br /><br /></div>

<div class="accordionButton"><b>Overview</b></div> <div class="accordionContent",><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Overview"><b>Here is a short overview of the two models.</b></a><br /><br /></div>

<div class="accordionButton"><b>Output Amplification Model</b></div> <div class="accordionContent"><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Michaelis_Menten"><b>Model based on Michaelis Menten Kinetics</b></a><br />Comparison between different amplification models (HIV1 and TEV) based on Michaelis Menten kinetics. However, Michaelis Menten kinetics does not apply to our system. Therefore, it had to be modelled from first principle (see below using law of mass action).<br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Michaelis_Menten#HIV1"><img src="http://www.openwetware.org/images/0/03/Slide2.JPG" height="150" width="200" alt="Model using HIV1"/></a> <a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Michaelis_Menten#TEV"><img src="http://www.openwetware.org/images/4/48/TEV.jpg" height="150" width="200" alt="Model using TEV"/></a><br /><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Mass_Action"><b>Model based on Law of Mass Action</b></a><br />Comparison between these 3 different models: Simple production, 1-step and 2-step amplification.<br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Mass_Action#Model_preA:_Simple_Production_of_Dioxygenase"><img src="http://www.openwetware.org/images/7/7f/Simple_production.JPG" height="100" width="300" alt="Simple Production"/></a> <a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Mass_Action#Model_A:_Activation_of_Dioxygenase_by_TEV_enzyme"><img src="http://www.openwetware.org/images/1/1c/1-step_amplification.JPG" height="100" width="300" alt="1-step amplification"/></a> <a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Mass_Action#Model_B:_Activation_of_Dioxygenase_by_TEV_or_activated_split_TEV_enzyme"><img src="http://www.openwetware.org/images/0/02/2-step_amplification.JPG" height="100" width="300" alt="2-step amplification"/></a><br /><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Variables1"><b>Variables and Constants</b></a><br />Here are the variables and constants that are used in the Output Amplification Model.<br /><br /></div>

<div class="accordionButton"><b>Protein Display Model</b></div> <div class="accordionContent"><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Protein_Display"><b>Protein Display Model</b></a><br />This is a model showing when the ComD receptor will be activated (after proteins have been cleaved).<br /><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Variables2"><b>Variables and Constants</b></a><br />Here are the variables and constants that are used in the Protein Display Model.<br /><br /></div>

<div class="accordionButton"><b>Feedback from Wetlab</b></div> <div class="accordionContent"><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Experiments1"><b>Experiments for the Output Amplification Model</b></a><br /><br /><a href="http://www.openwetware.org/wiki/IGEM:Imperial/2010/Experiments2"><b>Experiments for the Protein Display Model</b></a><br /><br /></div> </div>

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Engineering approach to project

Engineering cycle.jpg

1. Influence of Specification on Design and vice versa:

  • It was one of the longest steps as we were struggling to compromise the specifications with the viable designs.

2. Influence of Design on Modelling and vice versa:

  • All modelling done was meant to give answers to questions that arose in the design phase.
  • Once designs were chosen, they were modelled. It was found that 2 step amplification is not likely to be effiecient, so it was decided that only 1step amplification will be taken forward to assembly. This was a significant conclusion as it would take weeks in the labroatory to find that out.
  • The doubt about big enough gradient of AIPs to be established in the extracellular space to set off receptor was rationalised by modelling. The model allowed to determine conditions for the system to work

3. Influence of Modelling on Assembly and vice versa:

  • The results from modelling allowed to progress with assembly

4. Influence of Assembly on Testing and vice versa:

  • testing has been planned ahead, so assembly contructs have been modified to allow some testing methods like: purification or negative control.

5. Influence of Testing on Specifications and vice versa:

  • We did not get there yet. However, if the specifications would not be met by the results, we would need to try redesigning the system or, in case of no alternative, changing the specifications.

6. Influence of components not adjacent to each other in the cycle:

  • Testing may influence modelling as the results of the two do not match.
  • Many experiments were diesgned specifically on the request of modellers in order to find parameters for the models. Obtaining those paramters would increase the reliability of the models.