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Team:Calgary/Modelling/Method
From 2009.igem.org
(Difference between revisions)
| Line 126: | Line 126: | ||
<center><b>Table: Initial Values of the Species in the System</b> </center> | <center><b>Table: Initial Values of the Species in the System</b> </center> | ||
<br> | <br> | ||
| - | + | <table width="700" border="1" bgcolor="#414141" align = "center"> | |
<tr> | <tr> | ||
<td>Species</td> | <td>Species</td> | ||
| Line 135: | Line 135: | ||
<td>AI-2</td> | <td>AI-2</td> | ||
<td>0</td> | <td>0</td> | ||
| - | <td>Initially the amount of AI-2 is constant at 0. After an equilibruim is established variable amounts of AI-2 are added at different simulations.</td> | + | <td><align = "left">Initially the amount of AI-2 is constant at 0. After an equilibruim is established variable amounts of AI-2 are added at different simulations.</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
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<td>GFP</td> | <td>GFP</td> | ||
<td> 0</td> | <td> 0</td> | ||
| - | <td The model assumes that initially we have no GFP present . The simulation is allowed to run till the protein reaches equilibrium . The AI-2 is added after equilibrium conditions and a drop in GFP levels is observed.</td> | + | <td> The model assumes that initially we have no GFP present . The simulation is allowed to run till the protein reaches equilibrium . The AI-2 is added after equilibrium conditions and a drop in GFP levels is observed.</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 202: | Line 202: | ||
<td>The justification for the initial value of mRNA is the same as GFP</td> | <td>The justification for the initial value of mRNA is the same as GFP</td> | ||
</tr> | </tr> | ||
| - | </table | + | </table> |
<center><b> Table: The Kinetic Rate Constant Values</b> </center> | <center><b> Table: The Kinetic Rate Constant Values</b> </center> | ||
| - | + | <table width="200" border="1" bgcolor="#414141" align = "center"> | |
| + | <tr> | ||
| + | <td>Rate Constants</td> | ||
| + | <td>Constant Value</td> | ||
| + | <td>Rationale</td> | ||
| + | </tr> | ||
| + | |||
<tr> | <tr> | ||
| + | <td> kPhosU</td> | ||
<td> </td> | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>kPhosO</td> | ||
<td> </td> | <td> </td> | ||
<td> </td> | <td> </td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| + | <td>kTranscription</td> | ||
<td> </td> | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | |||
| + | <tr> | ||
| + | <td>kTranslation</td> | ||
<td> </td> | <td> </td> | ||
<td> </td> | <td> </td> | ||
</tr> | </tr> | ||
| - | + | <tr> | |
| + | <td>kProtDegrad</td> | ||
<td> </td> | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td> kAI2bind </td> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>kAI2unbind</td> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>kPQphosphatase</td> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>kNSPU</td> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>kNSPO</td> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>kPqrr4Sig54unbind</td> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>kPqrr4Sig54bind</td> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>kOPqrr4Unbind</td> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>kOPqrr4bind</td> | ||
| + | <td> </td> | ||
| + | <td> </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>kRNAdegrad</td> | ||
<td> </td> | <td> </td> | ||
<td> </td> | <td> </td> | ||
</tr> | </tr> | ||
| - | </table> | + | </table> |
| + | |||
<br> | <br> | ||
</td> | </td> | ||
Revision as of 00:50, 21 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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