Team:Bielefeld-CeBiTec/Results/Modelling/sourcecode

From 2014.igem.org

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<h6> Source Code </h6>
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<h2>main</h2>
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<h6>main</h6>
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function dy_dt = main_new(t, y, kcat, conc, km)<br>
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<br>
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dy_dt = zeros(6,1);<br>
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<br>
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%Michaelis-Menten kinetic<br>
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v1 = (kcat(1) * conc(1) * y(1)) / (km(1) + y(1)); %alsS<br>
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v2 = (kcat(2) * conc(2) * y(2)) / (km(2) + y(2)); %ilvC<br>
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v3 = (kcat(3) * conc(3) * y(3)) / (km(3) + y(3)); %ilvD<br>
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v4 = (kcat(4) * conc(4) * y(4)) / (km(4) + y(4)); %kivD<br>
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v5 = (kcat(5) * conc(5) * y(5)) / (km(5) + y(5)); %adhA<br>
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v6 = (kcat(6) * conc(6) * y(6)) / (km(6) + y(6)); %pyruvatase<br>
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v7 = (kcat(6) * conc(6) * y(6)) / (km(6) + y(6)); %pyruvatase<br>
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<br>
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<br>
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%differentiation systems<br>
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dy_dt(1) = -v1; %pyruvate<br>
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dy_dt(2) = v1 - 2*v2; %2-acetolactate<br>
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dy_dt(3) = v2 - v3; %2,3-dihydroxisovalerate<br>
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dy_dt(4) = v3 - v4; %2-ketoisovalerate<br>
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dy_dt(5) = v4 - v5; %isobutyraldehyde<br>
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dy_dt(6) = v5; %isobutanol<br>
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dy_dt(7) = v6 - v7; %pyruvate derivatives<br>
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<h6>solve</h6>
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%%%%%%%%%% INPUT %%%%%%%%%%%%%<br>
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<br>
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%timespan of the calculation [h]<br>
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timespan=[0,20];<br>
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<br>
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%starting conentrations [mM]:<br>
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sc = [10 0.0 0.0 0.0 0.06 0.0, 0.0];<br>
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<br>
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%kcat values [molecules per second]:<br>
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kcat = [8.9 3.6 185 10 10 150];<br>
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<br>
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%km values [mM]:<br>
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km = [13.6 0.25 1.5 5.02 9.1 0.1];<br>
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<br>
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%enzyme concentrations<br>
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conc = [1 0.9 0.8 0.7 0.6 0.5];<br>
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%improved enzyme concentrations<br>
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%conc = [1 0.9 0.8 3 4 0.5];<br>
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%metabolites:<br>
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%1= pyruvate<br>
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%2= 2-acetolactate<br>
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%3= 2,3-dihydroxyisovalerate<br>
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%4= 2-ketoisovalerate<br>
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%5= isobutyraldehyde<br>
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%6= isobutanol<br>
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%7= pyruvate derivatives<br>
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%%%%%%%%%%%%%% CALCULATION %%%%%%%%%%%%%%%<br>
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[T,Y] = ode45(@main_kcat, timespan, sc, [], kcat, conc, km);<br>
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%%%%%%%%%%%%%%% PLOTTING %%%%%%%%%%%%%%%%%%<br>
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plot(T,Y)<br>
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xlabel('time [h]')<br>
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ylabel('conzentraion [mM]')<br>
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legend('pyruvate','2-acetolactate','2,3-dihydroxyisovalerate','2-ketoisovalerate','isobutyraldehyde','isobutanol','pyruvate-derivatives')<br>
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Latest revision as of 19:15, 17 October 2014


Source Code

main

function dy_dt = main_new(t, y, kcat, conc, km)

dy_dt = zeros(6,1);

%Michaelis-Menten kinetic
v1 = (kcat(1) * conc(1) * y(1)) / (km(1) + y(1)); %alsS
v2 = (kcat(2) * conc(2) * y(2)) / (km(2) + y(2)); %ilvC
v3 = (kcat(3) * conc(3) * y(3)) / (km(3) + y(3)); %ilvD
v4 = (kcat(4) * conc(4) * y(4)) / (km(4) + y(4)); %kivD
v5 = (kcat(5) * conc(5) * y(5)) / (km(5) + y(5)); %adhA
v6 = (kcat(6) * conc(6) * y(6)) / (km(6) + y(6)); %pyruvatase
v7 = (kcat(6) * conc(6) * y(6)) / (km(6) + y(6)); %pyruvatase


%differentiation systems
dy_dt(1) = -v1; %pyruvate
dy_dt(2) = v1 - 2*v2; %2-acetolactate
dy_dt(3) = v2 - v3; %2,3-dihydroxisovalerate
dy_dt(4) = v3 - v4; %2-ketoisovalerate
dy_dt(5) = v4 - v5; %isobutyraldehyde
dy_dt(6) = v5; %isobutanol
dy_dt(7) = v6 - v7; %pyruvate derivatives

solve

%%%%%%%%%% INPUT %%%%%%%%%%%%%

%timespan of the calculation [h]
timespan=[0,20];

%starting conentrations [mM]:
sc = [10 0.0 0.0 0.0 0.06 0.0, 0.0];

%kcat values [molecules per second]:
kcat = [8.9 3.6 185 10 10 150];

%km values [mM]:
km = [13.6 0.25 1.5 5.02 9.1 0.1];

%enzyme concentrations
conc = [1 0.9 0.8 0.7 0.6 0.5];

%improved enzyme concentrations
%conc = [1 0.9 0.8 3 4 0.5];


%metabolites:
%1= pyruvate
%2= 2-acetolactate
%3= 2,3-dihydroxyisovalerate
%4= 2-ketoisovalerate
%5= isobutyraldehyde
%6= isobutanol
%7= pyruvate derivatives

%%%%%%%%%%%%%% CALCULATION %%%%%%%%%%%%%%%

[T,Y] = ode45(@main_kcat, timespan, sc, [], kcat, conc, km);


%%%%%%%%%%%%%%% PLOTTING %%%%%%%%%%%%%%%%%%
plot(T,Y)
xlabel('time [h]')
ylabel('conzentraion [mM]')
legend('pyruvate','2-acetolactate','2,3-dihydroxyisovalerate','2-ketoisovalerate','isobutyraldehyde','isobutanol','pyruvate-derivatives')

Retrieved from "http://2014.igem.org/Team:Bielefeld-CeBiTec/Results/Modelling/sourcecode"