"
Team:Calgary/Modelling/Method
From 2009.igem.org
(Difference between revisions)
| Line 112: | Line 112: | ||
[A] is the amount of reactant A present. <br><br> | [A] is the amount of reactant A present. <br><br> | ||
| - | The simulations were run for 50000 seconds . It was considered to be enough time for the system to reach equilibrium after disturbance. | + | The simulations were run for 50000 seconds . It was considered to be enough time for the system to reach equilibrium after disturbance. |
<br><br> | <br><br> | ||
<b>Sundial Solver</b> | <b>Sundial Solver</b> | ||
The sundial solver (SUNDIALS) was developed so that robust time integrators and non-linear solvers can be easily combined with already existing simulation codes. Minimal information from user is required and this solver allow users to easily supply their own data structures. The Sundials solvers are part of a third-party package developed at Lawrence Livermore National Laboratory. Built-in ordinary differential equation (ODE) solvers (ode45 and ode15s) are also part of the interface. | The sundial solver (SUNDIALS) was developed so that robust time integrators and non-linear solvers can be easily combined with already existing simulation codes. Minimal information from user is required and this solver allow users to easily supply their own data structures. The Sundials solvers are part of a third-party package developed at Lawrence Livermore National Laboratory. Built-in ordinary differential equation (ODE) solvers (ode45 and ode15s) are also part of the interface. | ||
<br><br> | <br><br> | ||
| - | When sundials solver is selected, the program selects one of teh two sundials solvers that suits your model: CVODE or IDA. CVODE is used for systems of ODEs (stiff or nonstiff) and this type of solver is usually used for a model that has no algebraic rules. IDA is a differential-algebraic equation (DAE) solver and it is usually used when there is one more algebraic rules. Since our model incorporates an event (the addition of autoinducer-II (AI-2)), this type of solver was used in our model. More information can be found here: https://computation.llnl.gov/casc/sundials/description/description.html | + | When sundials solver is selected, the program selects one of teh two sundials solvers that suits your model: CVODE or IDA. CVODE is used for systems of ODEs (stiff or nonstiff) and this type of solver is usually used for a model that has no algebraic rules. IDA is a differential-algebraic equation (DAE) solver and it is usually used when there is one more algebraic rules. Since our model incorporates an event (the addition of autoinducer-II (AI-2)), this type of solver was used in our model. More information can be found here: https://computation.llnl.gov/casc/sundials/description/description.html |
| Line 157: | Line 157: | ||
<td>LuxU:p</td> | <td>LuxU:p</td> | ||
<td>2</td> | <td>2</td> | ||
| - | <td> | + | <td>--</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 222: | Line 222: | ||
<tr> | <tr> | ||
<td> kPhosU</td> | <td> kPhosU</td> | ||
| - | <td> | + | <td>1.0E-6</td> |
<td> </td> | <td> </td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>kPhosO</td> | <td>kPhosO</td> | ||
| - | <td> | + | <td></td> |
<td> </td> | <td> </td> | ||
</tr> | </tr> | ||
| Line 243: | Line 243: | ||
<tr> | <tr> | ||
<td>kProtDegrad</td> | <td>kProtDegrad</td> | ||
| - | <td> | + | <td>2.8756E-4</td> |
| - | <td> | + | <td>The value was calculated from the estimated half life of the GFP in the gene circuit. </td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td> kAI2bind </td> | <td> kAI2bind </td> | ||
| - | <td> | + | <td>1.0</td> |
| - | <td> | + | <td>LuxP is a receptor for AI-2 therfore the binding is seen to be a fast process due to its specificity.</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>kAI2unbind</td> | <td>kAI2unbind</td> | ||
| - | <td> | + | <td>0.25</td> |
<td> </td> | <td> </td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>kPQphosphatase</td> | <td>kPQphosphatase</td> | ||
| - | <td> | + | <td>0.3</td> |
| - | <td> | + | <td>The dephosphorylation reaction is relatively fast due to the specificity of the protein LuxQ to LuxU:p.</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>kNSPU</td> | <td>kNSPU</td> | ||
| - | <td> | + | <td>0.09</td> |
| - | <td> | + | <td>This constant refers to the dephosphorylation of LuxU:p. The dephosphorylation is carried out by non-specific phosphatase.</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>kNSPO</td> | <td>kNSPO</td> | ||
| - | <td> | + | <td>0.09</td> |
| - | <td> | + | <td>The dephosphorylation of LuxO:p is carried out by non-specific phosphatase similar in the relationship to kNSPU. For this reason , the two parameter values are equal. </td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
Revision as of 22:59, 21 October 2009
UNIVERSITY OF CALGARY
|
MODELLING INDEX
|
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. |
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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.
 
k is the kinetic rate constant. The size of k will determine the speed of the reaction. A smaller value of k will produce a slow reaction rate while a larger value of k will produce a fast reaction rate. [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. Sundial Solver The sundial solver (SUNDIALS) was developed so that robust time integrators and non-linear solvers can be easily combined with already existing simulation codes. Minimal information from user is required and this solver allow users to easily supply their own data structures. The Sundials solvers are part of a third-party package developed at Lawrence Livermore National Laboratory. Built-in ordinary differential equation (ODE) solvers (ode45 and ode15s) are also part of the interface. When sundials solver is selected, the program selects one of teh two sundials solvers that suits your model: CVODE or IDA. CVODE is used for systems of ODEs (stiff or nonstiff) and this type of solver is usually used for a model that has no algebraic rules. IDA is a differential-algebraic equation (DAE) solver and it is usually used when there is one more algebraic rules. Since our model incorporates an event (the addition of autoinducer-II (AI-2)), this type of solver was used in our model. More information can be found here: https://computation.llnl.gov/casc/sundials/description/description.html 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
|
