Team:DTU-Denmark/Matlab

From 2011.igem.org

(Difference between revisions)
(Simulation)
(Simulation)
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== Simulation ==
== Simulation ==
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Temporal simulation is performed using the Systems Biology Toolbox 2 [[http://www.sbtoolbox.org/]] environment with numerical integration using ode45. The used models.
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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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[[File:DTU_Model7.txt]]
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[[File:DTU_Model8.txt]]
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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
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********** MODEL EVENTS
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event = gt(time,1), alpha_s, 40
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event = gt(time,3), alpha_r, 200
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event = gt(time,6), alpha_r, 0
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********** MODEL MATLAB FUNCTIONS
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</pre>
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[[File:DTU_Model7.txt|download]]
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 +
The partly stoichiometric model is specified by
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<pre style="height: 200px;">
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********** MODEL NAME
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Dimensionless form. Stoichiometric.
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********** MODEL NOTES
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Kinetic model of trap-RNA system.
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Parameters are estimated from literature.
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********** MODEL STATES
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d/dt(m) = 1 - m - k_s*alpha_m*m*s/(beta_m*beta_s)
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d/dt(s) = (beta_s/beta_m)*(alpha_s/alpha_m - s - k_r*alpha_m * s * r /(beta_s*beta_r))
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d/dt(r) = (beta_r/beta_m)*(alpha_r/alpha_m - r - k_r*alpha_m * s * r /(beta_s*beta_r))
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m(0) = 1
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s(0) = 0
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r(0) = 0                                   
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********** MODEL PARAMETERS
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alpha_m = 1
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alpha_s = 0
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alpha_r = 0
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beta_m = 0.0257
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beta_s = 0.0257
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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 [[1]] 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

File:DTU Model7.txt

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

File:DTU Model8.txt

The script running simulation and generating figures.