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From 2009.igem.org

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(){

// 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(){

 alert("hallo");

 // 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 N = 5;

 var K5 = 10;
 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) / (Math.pow(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 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 * Math.pow(((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 + Math.pow(data.ArsR[i],2))); data.ars2[i] = nonnegative((data.ars2T[i] * K3d) /(K3d + Math.pow(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]);

// ln is niet gedifineerd, alleen ln[2] wordt gebruikt is dit een array of een variable // Math.log(x) Math.LN2

//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] = data.GlpFT[i]; // mag deze wel negatief worden??
data.ArsBT[i+1] = nonnegative(data.ArsBT[i] + Timestep*(Beta4*data.ars1[i] - Math.LN2/(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]);

alert("data.ArsRT[i] "+ data.ArsRT[i]);

         data.ArsRT[i+1] = nonnegative(data.ArsRT[i] + Timestep*(Beta1*data.ars1[i] + Beta3*data.pro[i]-(Math.LN2/tauR)*data.ArsR[i]));
         data.GV[i+1] = nonnegative(data.GV[i] + Timestep*(Beta5*data.ars2[i] - Math.LN2*tauG*data.GV[i]));  
         data.Time[i+1] = nonnegative(data.Time[i] + Timestep);
 }

 var TotalmodelNode = document.getElementById("Totalmodel");
 TotalmodelNode.data = data;
 document.getElementById("TotalmodelGraph").refresh();

} // end function modeltotal

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