Team:Groningen/Modelling/model/calc.js

From 2009.igem.org

(Difference between revisions)
(het gehele model)
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function transport(){
function transport(){
 +
 +
alert("Hallo");
  // variablen
  // variablen
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function modelTotal(){
function modelTotal(){
-
   alert("modelTotal");
+
 
 +
// Definieren van begincondities dit zijn dus constanten die later niet gebruikt worden
 +
//Begincondities (op tijdstip nul) die in het 0-de element van een array moeten worden gezet.
 +
var data = {
 +
AsexT:  [5],
 +
ArsBas: [0],
 +
GlpFas: [0],
 +
GlpFT:  [5],
 +
ArsBT:  [5],
 +
AsinT:  [0],
 +
ars1T:  [5],
 +
ars2T:  [5],
 +
pro:    [5],
 +
ArsRT:  [5],
 +
GV:    [0],
 +
Time:   [0],
 +
ArsB:  [0],
 +
Asin:  [0],
 +
ArsR:  [0],
 +
ars:  [0],
 +
GlpF:  [0],
 +
ArsRas:[0],
 +
ars1:  [0],
 +
ars2:  [0],
 +
arsT:  [0],
 +
ArsRars:[0],
 +
Asex:  [0]
 +
 
 +
};
 +
 
 +
 
 +
// Begincondities die constantes blijven
 +
var Vc = 10;
 +
var TotalTime = 10;  // 10 seconds
 +
var Timestep = 0.01; // 1/100th of a second
 +
var N = TotalTime/Timestep;
 +
var Vs = 10;
 +
var K7 = 10;
 +
var k8 = 10;
 +
var v5 = 10;
 +
var tauG = 10;
 +
var tauB = 10;
 +
var tauR = 10;
 +
var Beta5 = 10;
 +
var Beta4 = 10;
 +
var Beta3 = 10;
 +
var Beta1 = 10;
 +
var K3d = 0,33; // micromolair;
 +
var K1d = K3d/10;
 +
 
 +
//Er komen nog een hoop nieuwe variabelen aan stop ze tenzij anders aangegeven allemaal in een Array
 +
//We stoppen nu het gehele programma in een loop (Ik doe een forloop, je moet zelf maar kijken wat het handigst is.)
 +
var TOL = 10^-6;
 +
var getal = 500;
 +
 
 +
 
 +
 
 +
function nonnegative(v) { /*return v>=0?v:0;*/ return v; }
 +
 
 +
for(var i = 0 ; i < N ; i++) {
 +
//We passen nu eerst Newton's methode toe
 +
// Eerst maken we een Array X met de Afschatting van de variabelen
 +
 
 +
var x =new Array(7);
 +
x[0] = data.ArsBT[i]/2; //(ArsB)
 +
x[1] = data.Asex[i]/10; // Asin       
 +
x[2] = data.ArsRT[i]/3; // ArsR
 +
x[3] = data.ArsRT[i]/3; // ars
 +
x[4] = data.GlpF[i]/2; // GlpF       
 +
x[5] = data.ArsRT[i]/3; // ArsRas
 +
x[6] = data.Asex[i]/2;  // Asex     
 +
 
 +
//Nu maken we weer een forloop aan
 +
var Yvalue = TOL+1;
 +
for ( var j = 1; j <= N && Yvalue>TOL; j++) {
 +
 +
var F =new Array(6);
 +
F[0] =  ((data.ArsBT[i] * K7) / (x[1] + K7)) - x[0]
 +
F[1] = ((data.AsinT[i]) / (1 + (x[2] / K1d) + (x[0]) / K7))) - X[1];
 +
F[2] = ((data.ArsRT[i]) / (1 + (x[1] / K1d) + (2 * x[2] * x[3] / K3d))) - x[2];
 +
F[3] = ((K3d) / (x[2]^2 + K3d)) - x[3] ;
 +
F[4] = ((data.GlpFT[i] * K5) / (x(6) + K5)) - x[4];
 +
F[5] = ((data.ArsRT[i] * x[1] / K1d) / (1 + (x[1] / K1d) + (2 * x[2] * x[3] / K3d))) - x[5];
 +
F[6] = ((data.AsexT[i] * K5) / (K5 + x[4])) - x[6];
 +
 +
//Hierna maken we een Matrix 7x7 matrix J aan
 +
var matrix = new Array(7);
 +
matrix[0] = new Array(7);
 +
matrix[1] = new Array(7);
 +
matrix[2] = new Array(7);
 +
matrix[3] = new Array(7);
 +
matrix[4] = new Array(7);
 +
matrix[5] = new Array(7);
 +
matrix[6] = new Array(7);
 +
 +
 
 +
matrix[0][0] = -1;  matrix[0][1] = 0; matrix[0][2] = 0; matrix[0][3] = 0; matrix[0][4] = 0; matrix[0][5] = 0; matrix[0][6] = 0;
 +
matrix[1][0] = 0;  matrix[1][1] = -1; matrix[1][2] = 0; matrix[1][3] = 0; matrix[1][4] = 0; matrix[1][5] = 0; matrix[1][6] = 0;
 +
matrix[2][0] = 0;  matrix[2][1] = 0; matrix[2][2] = (-2 * ((data.ArsRT[i]) / (1 + (x[1] / K1d) + (2 * x[2] * x[3] / K3d))^2) - 1); matrix[2][3] = 0; matrix[2][4] = 0; matrix[2][5] = 0; matrix[2][6] = 0;
 +
matrix[3][0] = 0;  matrix[3][1] = 0; matrix[3][2] = 0; matrix[3][3] = -1; matrix[3][4] = 0; matrix[3][5] = 0; matrix[3][6] = 0;
 +
matrix[4][0] = 0;  matrix[4][1] = 0; matrix[4][2] = 0; matrix[4][3] = 0; matrix[4][4] = -1; matrix[4][5] = 0; matrix[4][6] = 0;
 +
matrix[5][0] = 0;  matrix[5][1] = 0; matrix[5][2] = 0; matrix[5][3] = 0; matrix[5][4] = 0; matrix[5][5] = -1; matrix[5][6] = 0;
 +
matrix[6][0] = 0;  matrix[6][1] = 0; matrix[6][2] = 0; matrix[6][3] = 0; matrix[6][4] = 0; matrix[6][5] = 0; matrix[6][6] = -1;
 +
 +
//Nu maken we een Array Y aan
 +
var y =new Array(7);
 +
y[0] = F[0]/ matrix[0][0];
 +
y[1] = F[1]/ matrix[1][1];
 +
y[2] = F[2]/ matrix[2][2];
 +
y[3] = F[3]/ matrix[3][3];
 +
y[4] = F[4]/ matrix[4][4];
 +
y[5] = F[5]/ matrix[5][5];
 +
y[6] = F[6]/ matrix[6][6];
 +
 +
// Math.abs om de Y waarden zetten (bijv. Math.abs(Y(0)))
 +
Yvalue = Math.abs(y[0]) + Math.abs(y[1]) + Math.abs(y[2]) + Math.abs(y[3]) + Math.abs(y[4]) + Math.abs(y[5]) + Math.abs(y[6]);
 +
 +
for (var k = 0 ; k <= 6 ; k++) {
 +
x[k] = x[k] + y[k];
 +
}
 +
}
 +
 
 +
data.ArsB[i]  = nonnegative(x[0]);
 +
data.Asin[i]  = nonnegative(x[1]);
 +
data.ArsR[i]  = nonnegative(x[2]);
 +
data.ars[i]    = nonnegative(x[3]);
 +
data.GlpF[i]  = nonnegative(x[4]);
 +
data.ArsRas[i] = nonnegative(x[5]);
 +
data.Asex[i]  = nonnegative(x[6]);
 +
 +
 
 +
//Nu gaan we verdere variabelen opstellen ook deze moeten weer in Array's komen te staan
 +
var k6 = (v5 * Vc) / (data.GlpFT[i] * Vs);
 +
data.ars1[i] = nonnegative(  (data.ars1T[i] * K3d) /(K3d + data.ArsR[i]^2)  );
 +
data.ars2[i] = nonnegative((data.ars2T[i] * K3d) /(K3d + data.ArsR[i]^2));
 +
 +
data.ArsBas[i] = nonnegative(data.ArsBT[i] - data.ArsB[i]);
 +
data.GlpFas[i] = nonnegative(data.GlpFT[i] - data.GlpF[i]);
 +
data.arsT[i] = nonnegative(data.ars1T[i] + data.ars2T[i]);
 +
data.ArsRars[i] = nonnegative(data.arsT[i] - data.ars[i]);
 +
data.Asex[i] = nonnegative(data.AsexT[i] - data.GlpFas[i]);
 +
 
 +
 
 +
//We gaan nu met Eulers methode de volgende slag voorbereiden
 +
data.AsexT[i+1] = nonnegative(data.AsexT[i] + Timestep((Vc/Vs)*k8*data.ArsBas[i]-k6*data.GlpFas[i]));
 +
data.GlpFT[i+1] = GlpFT[i]; // mag deze wel negative worden??
 +
data.ArsBT[i+1] = nonnegative(data.ArsBT[i] + Timestep*(Beta4*data.ars1[i] - Ln[2]/(tauB * data.ArsB[i])));
 +
data.AsinT[i+1] = nonnegative(data.AsinT[i] + Timestep*((Vs/Vc)*k6*data.GlpFas[i]-k8*data.ArsBas[i]));
 +
data.ars1T[i+1] = nonnegative(data.ars1T[i]);
 +
data.ars2T[i+1] = nonnegative(data.ars2T[i]);
 +
data.pro[i+1] = nonnegative(data.pro[i]);
 +
data.ArsRT[i+1] = nonnegative(data.ArsRT[i] + Timestep(Beta1*data.ars1[i] + Beta3*data.pro[i] - (ln[2]/tauR)*data.ArsR[i]));
 +
data.GV[i+1] = nonnegative(data.GV[i] + Timestep(Beta5*data.ars2[i] - ln[2]*tauG*data.GV[i]));
 +
data.Time[i+1] = nonnegative(data.Time[i] + Timestep);
 +
 
 +
}
 +
 
 +
 
 +
 
 +
 
 +
 
} // end function
} // end function

Revision as of 10:06, 9 September 2009

function calc(){ 

 //  gets input
 var growthFactorNode = document.getElementById("growthFactor");

 // reads input
 var growthFactor = Number(growthFactorNode.value); 
 
 // begin variable
 var time = 0;
 var x = 0;
 var y = 0;
 arrValueX = new Array();
 arrValueY = new Array();



 // process
 var growthFactor = growthFactor + 1;
 for (var time = 0; time < 30; time++) {
   var y = growthFactor*x*x;
   var x = x + 1;
   arrValueX.push(x);
   arrValueY.push(y);
 }
 

 // Set outputs
 setOutput(growthFactorAnswer, growthFactor ); 
 document.getElementById('modelDataGraph').refresh();

}


function setOutput(node,v) { 

 node.innerHTML = formatNumberToHTML(v);
 node.value = v;

}


function formatNumberToHTML(v,p) { 

 if (p===undefined) p = 5;
 return v.toPrecision(p)
         .replace(/e\+([0-9]+)$/i,'·10$1')
         .replace(/e\-([0-9]+)$/i,'·10-$1');

}


// ------ Annelies timer functie ---------

var mijnTimer;

function tijd(){ 

 //  gets input
 var timeMiliSecNode = document.getElementById("timeMiliSec");
 // reads input
 var timeMiliSec2 = Number(timeMiliSecNode.value); 

 //alert("functie tijd: "+timeMiliSec2);

 if (mijnTimer) clearInterval(mijnTimer);
 mijnTimer = setInterval( "doSomething()",timeMiliSec2);

}

function doSomething(){ 

   //alert("functie doe iets BOVEN DE IF LUS: "+doSomething.time);

   if (doSomething.time === undefined) {

     doSomething.time = 0;
     
     //alert("functie doe ietsFDBADFNA: "+doSomething.time);
   }

   // Set outputs
   setOutput(tijdAnswer, doSomething.time);
   doSomething.time += 1;
  
   transport();

}



// -------- transport model, geeft waarden mee in een object/array ----------


function transport(){

alert("Hallo"); 

// variablen
 var data = {time: [0],
             AsIn: [0],
             ArsB: [5],
             AsEx: [5],
             GlpF: [5],
             GlpFAs: [0],
             ArsBAs: [0]};

// constanten 

 var totalTime = 300;
 var stepSize = 0.1;
 var K5on = 1;
 var K5off = 1e-6;
 var K6 = 1e-3;
 var Vc = 1.1 - 0.0073;
 var Vs = 0.0073;
 var K7on = 1;
 var K7off = 1e-6;
 var K8 = 1e-3;



 var N = totalTime / stepSize ;

 for (var i=1;i<=N;i++){
   data.GlpFAs[i] = data.GlpFAs[i-1] + stepSize * (K5on * data.AsEx[i-1] * data.GlpF[i-1] - (K5off + K6) * data.GlpFAs[i-1]);
   data.AsEx[i] = data.AsEx[i-1] + stepSize * (-K5on * data.AsEx[i-1] * data.GlpF[i-1] + K5off * data.GlpFAs[i-1] + (Vc/Vs) * K8 * data.ArsBAs[i-1]);
   data.GlpF[i] = data.GlpF[i-1] + stepSize * (-(K5on * data.AsEx[i-1] * data.GlpF[i-1] - (K5off + K6) * data.GlpFAs[i-1]));
   data.ArsBAs[i] = data.ArsBAs[i-1] + stepSize * (K7on * data.AsIn[i-1] * data.ArsB[i-1] - (K7off+K8) * data.ArsBAs[i-1]);
   data.AsIn[i] = data.AsIn[i-1] + stepSize * (-K7on * data.AsIn[i-1] * data.ArsB[i-1] - (K7off + K8) * data.ArsBAs[i-1] - K8 * data.ArsBAs[i-1] + (Vs/Vc) * K6 * data.GlpFAs[i-1]);
   data.ArsB[i] = data.ArsB[i-1] + stepSize * (-(K7on * data.AsIn[i-1] * data.ArsB[i-1] - (K7off + K8) * data.ArsBAs[i-1]));
   data.time[i] = data.time[i-1] + stepSize;
 }

 setOutput(ModelAnswer, data.AsEx[4]); 
 var modelDataNode = document.getElementById("modelData");
 modelDataNode.data = data;

 document.getElementById("modelDataGraph").refresh();

}


// ------- het gehele model -------------------------------------------


function modelTotal(){

// Definieren van begincondities dit zijn dus constanten die later niet gebruikt worden //Begincondities (op tijdstip nul) die in het 0-de element van een array moeten worden gezet. var data = { AsexT: [5], ArsBas: [0], GlpFas: [0], GlpFT: [5], ArsBT: [5], AsinT: [0], ars1T: [5], ars2T: [5], pro: [5], ArsRT: [5], GV: [0], Time: [0], ArsB: [0], Asin: [0], ArsR: [0], ars: [0], GlpF: [0], ArsRas:[0], ars1: [0], ars2: [0], arsT: [0], ArsRars:[0], Asex: [0]

};


// Begincondities die constantes blijven var Vc = 10; var TotalTime = 10; // 10 seconds var Timestep = 0.01; // 1/100th of a second var N = TotalTime/Timestep; var Vs = 10; var K7 = 10; var k8 = 10; var v5 = 10; var tauG = 10; var tauB = 10; var tauR = 10; var Beta5 = 10; var Beta4 = 10; var Beta3 = 10; var Beta1 = 10; var K3d = 0,33; // micromolair; var K1d = K3d/10;

//Er komen nog een hoop nieuwe variabelen aan stop ze tenzij anders aangegeven allemaal in een Array //We stoppen nu het gehele programma in een loop (Ik doe een forloop, je moet zelf maar kijken wat het handigst is.) var TOL = 10^-6; var getal = 500;


function nonnegative(v) { /*return v>=0?v:0;*/ return v; }

for(var i = 0 ; i < N ; i++) { //We passen nu eerst Newton's methode toe // Eerst maken we een Array X met de Afschatting van de variabelen

var x =new Array(7); x[0] = data.ArsBT[i]/2; //(ArsB) x[1] = data.Asex[i]/10; // Asin x[2] = data.ArsRT[i]/3; // ArsR x[3] = data.ArsRT[i]/3; // ars x[4] = data.GlpF[i]/2; // GlpF x[5] = data.ArsRT[i]/3; // ArsRas x[6] = data.Asex[i]/2; // Asex

//Nu maken we weer een forloop aan var Yvalue = TOL+1; for ( var j = 1; j <= N && Yvalue>TOL; j++) {

var F =new Array(6); F[0] = ((data.ArsBT[i] * K7) / (x[1] + K7)) - x[0] F[1] = ((data.AsinT[i]) / (1 + (x[2] / K1d) + (x[0]) / K7))) - X[1]; F[2] = ((data.ArsRT[i]) / (1 + (x[1] / K1d) + (2 * x[2] * x[3] / K3d))) - x[2]; F[3] = ((K3d) / (x[2]^2 + K3d)) - x[3] ; F[4] = ((data.GlpFT[i] * K5) / (x(6) + K5)) - x[4]; F[5] = ((data.ArsRT[i] * x[1] / K1d) / (1 + (x[1] / K1d) + (2 * x[2] * x[3] / K3d))) - x[5]; F[6] = ((data.AsexT[i] * K5) / (K5 + x[4])) - x[6];

//Hierna maken we een Matrix 7x7 matrix J aan var matrix = new Array(7); matrix[0] = new Array(7); matrix[1] = new Array(7); matrix[2] = new Array(7); matrix[3] = new Array(7); matrix[4] = new Array(7); matrix[5] = new Array(7); matrix[6] = new Array(7);


matrix[0][0] = -1; matrix[0][1] = 0; matrix[0][2] = 0; matrix[0][3] = 0; matrix[0][4] = 0; matrix[0][5] = 0; matrix[0][6] = 0; matrix[1][0] = 0; matrix[1][1] = -1; matrix[1][2] = 0; matrix[1][3] = 0; matrix[1][4] = 0; matrix[1][5] = 0; matrix[1][6] = 0; matrix[2][0] = 0; matrix[2][1] = 0; matrix[2][2] = (-2 * ((data.ArsRT[i]) / (1 + (x[1] / K1d) + (2 * x[2] * x[3] / K3d))^2) - 1); matrix[2][3] = 0; matrix[2][4] = 0; matrix[2][5] = 0; matrix[2][6] = 0; matrix[3][0] = 0; matrix[3][1] = 0; matrix[3][2] = 0; matrix[3][3] = -1; matrix[3][4] = 0; matrix[3][5] = 0; matrix[3][6] = 0; matrix[4][0] = 0; matrix[4][1] = 0; matrix[4][2] = 0; matrix[4][3] = 0; matrix[4][4] = -1; matrix[4][5] = 0; matrix[4][6] = 0; matrix[5][0] = 0; matrix[5][1] = 0; matrix[5][2] = 0; matrix[5][3] = 0; matrix[5][4] = 0; matrix[5][5] = -1; matrix[5][6] = 0; matrix[6][0] = 0; matrix[6][1] = 0; matrix[6][2] = 0; matrix[6][3] = 0; matrix[6][4] = 0; matrix[6][5] = 0; matrix[6][6] = -1;

//Nu maken we een Array Y aan var y =new Array(7); y[0] = F[0]/ matrix[0][0]; y[1] = F[1]/ matrix[1][1]; y[2] = F[2]/ matrix[2][2]; y[3] = F[3]/ matrix[3][3]; y[4] = F[4]/ matrix[4][4]; y[5] = F[5]/ matrix[5][5]; y[6] = F[6]/ matrix[6][6];

// Math.abs om de Y waarden zetten (bijv. Math.abs(Y(0))) Yvalue = Math.abs(y[0]) + Math.abs(y[1]) + Math.abs(y[2]) + Math.abs(y[3]) + Math.abs(y[4]) + Math.abs(y[5]) + Math.abs(y[6]);

for (var k = 0 ; k <= 6 ; k++) { x[k] = x[k] + y[k]; } }

data.ArsB[i] = nonnegative(x[0]); data.Asin[i] = nonnegative(x[1]); data.ArsR[i] = nonnegative(x[2]); data.ars[i] = nonnegative(x[3]); data.GlpF[i] = nonnegative(x[4]); data.ArsRas[i] = nonnegative(x[5]); data.Asex[i] = nonnegative(x[6]);


//Nu gaan we verdere variabelen opstellen ook deze moeten weer in Array's komen te staan var k6 = (v5 * Vc) / (data.GlpFT[i] * Vs); data.ars1[i] = nonnegative( (data.ars1T[i] * K3d) /(K3d + data.ArsR[i]^2) ); data.ars2[i] = nonnegative((data.ars2T[i] * K3d) /(K3d + data.ArsR[i]^2));

data.ArsBas[i] = nonnegative(data.ArsBT[i] - data.ArsB[i]); data.GlpFas[i] = nonnegative(data.GlpFT[i] - data.GlpF[i]); data.arsT[i] = nonnegative(data.ars1T[i] + data.ars2T[i]); data.ArsRars[i] = nonnegative(data.arsT[i] - data.ars[i]); data.Asex[i] = nonnegative(data.AsexT[i] - data.GlpFas[i]);


//We gaan nu met Eulers methode de volgende slag voorbereiden data.AsexT[i+1] = nonnegative(data.AsexT[i] + Timestep((Vc/Vs)*k8*data.ArsBas[i]-k6*data.GlpFas[i])); data.GlpFT[i+1] = GlpFT[i]; // mag deze wel negative worden?? data.ArsBT[i+1] = nonnegative(data.ArsBT[i] + Timestep*(Beta4*data.ars1[i] - Ln[2]/(tauB * data.ArsB[i]))); data.AsinT[i+1] = nonnegative(data.AsinT[i] + Timestep*((Vs/Vc)*k6*data.GlpFas[i]-k8*data.ArsBas[i])); data.ars1T[i+1] = nonnegative(data.ars1T[i]); data.ars2T[i+1] = nonnegative(data.ars2T[i]); data.pro[i+1] = nonnegative(data.pro[i]); data.ArsRT[i+1] = nonnegative(data.ArsRT[i] + Timestep(Beta1*data.ars1[i] + Beta3*data.pro[i] - (ln[2]/tauR)*data.ArsR[i])); data.GV[i+1] = nonnegative(data.GV[i] + Timestep(Beta5*data.ars2[i] - ln[2]*tauG*data.GV[i])); data.Time[i+1] = nonnegative(data.Time[i] + Timestep);

}



} // end function

Retrieved from "http://2009.igem.org/Team:Groningen/Modelling/model/calc.js"