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Team:Calgary/Modelling/Method
From 2009.igem.org
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[A] is the amount of reactant A present. <br> | [A] is the amount of reactant A present. <br> | ||
| - | The simulations were run for 50000 seconds . It was considered to be enough time for the system to reach equilibrium.<i> The Sundials Solver (how do they work ?)was used to run these simulations because for this model it was considered to produce optimal results. (how do simulations work?)</i> | + | The simulations were run for 50000 seconds . It was considered to be enough time for the system to reach equilibrium after disturbance.<i> The Sundials Solver (how do they work ?)was used to run these simulations because for this model it was considered to produce optimal results. (how do simulations work?)</i> |
</div> | </div> | ||
| Line 124: | Line 124: | ||
<div class="desc"> | <div class="desc"> | ||
</div> | </div> | ||
| - | <center>Table: Initial Values of the Species in the System </center> | + | <center><b>Table: Initial Values of the Species in the System</b> </center> |
<br> | <br> | ||
| - | <center> Table: The Kinetic Rate Constant Values </center> | + | <center><table width="400" border="1" bgcolor="#414141"> |
| + | <tr> | ||
| + | <td>Species</td> | ||
| + | <td>Initial Value</td> | ||
| + | <td>Rationale</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>AI-2</td> | ||
| + | <td>0</td> | ||
| + | <td>Initially the amount of AI-2 is constant. After an equilibruim is established variable amounts of AI-2 is added.</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>LuxPQ</td> | ||
| + | <td>10</td> | ||
| + | <td>The amount of LuxPQ varies depending on the simulation run. </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>AI-2:LuxPQ</td> | ||
| + | <td>0</td> | ||
| + | <td>This value is kept 0 at time = 0 because the initial concentration of AI-2 is 0. </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>LuxU:p</td> | ||
| + | <td>2</td> | ||
| + | <td>----</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>LuxU</td> | ||
| + | <td>1000</td> | ||
| + | <td>There is a lot of this species present in the cell in nature. To signify plenty we assign it a value 1000.</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>LuxO:p</td> | ||
| + | <td>2</td> | ||
| + | <td>Equal amounts of LuxO:p and LuxU:p was considered in the model because LuxU:p phosphorylates LuxO . The phosphorylation reaction is considered to be a fast reaction therefore there are equal amounts of the two protein.</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>LuxO:p</td> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>p</td> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>sigma54</td> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>sigma54:LuxO:p:Pqrr4</td> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>Sigma54:Pqrr4</td> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>Pqrr4</td> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>GFP</td> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>mRNA</td> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | </table></center> | ||
| + | <center><b> Table: The Kinetic Rate Constant Values</b> </center> | ||
| + | <center><table width="200" border="1" bgcolor="#414141"> | ||
| + | <tr> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | </table></center> | ||
<br> | <br> | ||
</td> | </td> | ||
Revision as of 18:21, 20 October 2009
UNIVERSITY OF CALGARY
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MODELLING INDEX
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A TOUR OF THE UNIVERSITY OF CALGARY iGEM TEAM
We've reached modelling, the fifth stop on our tour! We've looked in to two different methods of modelling our system: Differential Equation Based Modelling and Membrane Computing. Here, you can explore the similarities and differences, as well as the functions of each method. As well, you can find the results of our characterization of the signalling pathway. Once you're done, we'll move on to the Second Life component of the project HERE. |
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DIFFERENTIAL EQUATIONS MODELLING METHODS
The simbiology interface from Matlab was used to simulate the differential equations model. Chemical Kinetic equations were used to build the model for simulation.
 
[A] is the amount of reactant A present. The simulations were run for 50000 seconds . It was considered to be enough time for the system to reach equilibrium after disturbance. The Sundials Solver (how do they work ?)was used to run these simulations because for this model it was considered to produce optimal results. (how do simulations work?) The Reactions
The system was represented by the following reactions. The reactions with double headed arrows have two rate constants(forward/ reverse rate constant). All reactions were assumed to be elementary reactions.
Parameter Rationale
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