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Team:DTU-Denmark/Matlab
From 2011.igem.org
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== Simulation == | == Simulation == | ||
| - | Temporal simulation is performed using the Systems Biology Toolbox 2 [[http://www.sbtoolbox.org/]] environment with numerical integration using ode45. The | + | Temporal simulation is performed using the Systems Biology Toolbox 2 [[http://www.sbtoolbox.org/]] environment with numerical integration using ode45. The catalytical model is specified by |
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<pre style="height: 200px;"> | <pre style="height: 200px;"> | ||
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k_s = 0.00082 | k_s = 0.00082 | ||
k_r = 0.0082 | k_r = 0.0082 | ||
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********** MODEL VARIABLES | ********** MODEL VARIABLES | ||
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********** MODEL REACTIONS | ********** MODEL REACTIONS | ||
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********** MODEL FUNCTIONS | ********** MODEL FUNCTIONS | ||
| + | ********** MODEL EVENTS | ||
| + | event = gt(time,1), alpha_s, 40 | ||
| + | event = gt(time,3), alpha_r, 200 | ||
| + | event = gt(time,6), alpha_r, 0 | ||
| + | ********** MODEL MATLAB FUNCTIONS | ||
| + | </pre> | ||
| + | [[File:DTU_Model7.txt|download]] | ||
| + | |||
| + | The partly stoichiometric model is specified by | ||
| + | |||
| + | <pre style="height: 200px;"> | ||
| + | ********** MODEL NAME | ||
| + | Dimensionless form. Stoichiometric. | ||
| + | |||
| + | ********** MODEL NOTES | ||
| + | Kinetic model of trap-RNA system. | ||
| + | Parameters are estimated from literature. | ||
| + | |||
| + | ********** MODEL STATES | ||
| + | d/dt(m) = 1 - m - k_s*alpha_m*m*s/(beta_m*beta_s) | ||
| + | d/dt(s) = (beta_s/beta_m)*(alpha_s/alpha_m - s - k_r*alpha_m * s * r /(beta_s*beta_r)) | ||
| + | d/dt(r) = (beta_r/beta_m)*(alpha_r/alpha_m - r - k_r*alpha_m * s * r /(beta_s*beta_r)) | ||
| + | |||
| + | m(0) = 1 | ||
| + | s(0) = 0 | ||
| + | r(0) = 0 | ||
| + | |||
| + | ********** MODEL PARAMETERS | ||
| + | alpha_m = 1 | ||
| + | alpha_s = 0 | ||
| + | alpha_r = 0 | ||
| + | beta_m = 0.0257 | ||
| + | beta_s = 0.0257 | ||
| + | beta_r = 0.0257 | ||
| + | k_s = 0.00082 | ||
| + | k_r = 0.0082 | ||
| + | |||
| + | ********** MODEL VARIABLES | ||
| + | |||
| + | ********** MODEL REACTIONS | ||
| + | |||
| + | ********** MODEL FUNCTIONS | ||
********** MODEL EVENTS | ********** MODEL EVENTS | ||
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********** MODEL MATLAB FUNCTIONS | ********** MODEL MATLAB FUNCTIONS | ||
</pre> | </pre> | ||
| + | |||
| + | [[File:DTU_Model8.txt|download]] | ||
The script running simulation and generating figures. | The script running simulation and generating figures. | ||
{{:Team:DTU-Denmark/Templates/Standard_page_end}} | {{:Team:DTU-Denmark/Templates/Standard_page_end}} | ||
Revision as of 02:29, 22 September 2011
Matlab code
Simulation
Temporal simulation is performed using the Systems Biology Toolbox 2 http://www.sbtoolbox.org/ environment with numerical integration using ode45. The catalytical model is specified by
********** MODEL NAME Dimensionless form. Catalytical. ********** MODEL NOTES Kinetic model of trap-RNA system. Parameters are estimated from literature. ********** MODEL STATES d/dt(m) = 1 - m - k_s*alpha_m*m*s/(beta_m*beta_s) d/dt(s) = (beta_s/beta_m)*(alpha_s/alpha_m - s - k_r*alpha_m * s * r /(beta_s*beta_r)) d/dt(r) = (beta_r/beta_m)*(alpha_r/alpha_m - r) m(0) = 1 s(0) = 0 r(0) = 0 ********** MODEL PARAMETERS alpha_m = 10 alpha_s = 0 alpha_r = 0 beta_m = 0.0257 beta_s = 0.0257 beta_r = 0.0257 k_s = 0.00082 k_r = 0.0082 ********** MODEL VARIABLES ********** MODEL REACTIONS ********** MODEL FUNCTIONS ********** MODEL EVENTS event = gt(time,1), alpha_s, 40 event = gt(time,3), alpha_r, 200 event = gt(time,6), alpha_r, 0 ********** MODEL MATLAB FUNCTIONS
The partly stoichiometric model is specified by
********** MODEL NAME Dimensionless form. Stoichiometric. ********** MODEL NOTES Kinetic model of trap-RNA system. Parameters are estimated from literature. ********** MODEL STATES d/dt(m) = 1 - m - k_s*alpha_m*m*s/(beta_m*beta_s) d/dt(s) = (beta_s/beta_m)*(alpha_s/alpha_m - s - k_r*alpha_m * s * r /(beta_s*beta_r)) d/dt(r) = (beta_r/beta_m)*(alpha_r/alpha_m - r - k_r*alpha_m * s * r /(beta_s*beta_r)) m(0) = 1 s(0) = 0 r(0) = 0 ********** MODEL PARAMETERS alpha_m = 1 alpha_s = 0 alpha_r = 0 beta_m = 0.0257 beta_s = 0.0257 beta_r = 0.0257 k_s = 0.00082 k_r = 0.0082 ********** MODEL VARIABLES ********** MODEL REACTIONS ********** MODEL FUNCTIONS ********** MODEL EVENTS event = gt(time,1), alpha_s, 40 event = gt(time,3), alpha_r, 200 event = gt(time,6), alpha_r, 0 ********** MODEL MATLAB FUNCTIONS
The script running simulation and generating figures.
Sponsors
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