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From 2013.igem.org

/** background processing

• /

       var ProteinGazPromoterStrength = 1;
       var ProteinGazSize = 4;
       var ProteinGazHalfLife = 20;
       var ProteinGazThreshold = 25; // = SynthesisThreshold
       var ProteinGazTimeConstant = 3;

       var GasProductionFactor = 1;
       var GasDissipation = 39.5;
       
       var RepressorPromoterStrength = 4;
       var RepressorSize = 1;
       var RepressorHalfLife = 20;
       var RepressorThreshold = 25; //Q max ~ 100
       var RepressorTimeConstant = 3;
       
       var AhlrPromoterStrength = 4;
       var AhlrSize = 1;
       var AhlrHalfLife = 10;
       var AhlrThreshold = 10; //Q max ~ 100
       var AhlrTimeConstant = 2;
       
       var AhlPromoterStrength = 4;
       var AhlSize = 1;
       var AhlHalfLife = 10;
       var AhlThreshold = 10; //Q max ~ 100
       var AhlTimeConstant = 2;
       
       
       var ProteinGazQuantity = 0;
       var RepressorQuantity = 0;
       var GasQuantity = 0;
       var AhlrQuantity = 0;
       var AhlQuantity = 0;
       
       var nowProteinGazQuantity = 0;
       var nowRepressorQuantity = 0;
       var nowGasQuantity = 0;
       var nowAhlrQuantity = 0;
       
       var DELTA_TIME = 0.125;
       var SAMPLE_POINTS = 3200;

       function GetNextProteinGazQuantity()
       {
           nowProteinGazQuantity = ProteinGazQuantity;
           ProteinGazQuantity += GetProteinGazRate() * DELTA_TIME;
           if (ProteinGazQuantity < 0)
               ProteinGazQuantity = 0;
           return nowProteinGazQuantity ;
       }

       function GetNextRepressorQuantity()
       {
           nowRepressorQuantity = RepressorQuantity;
           RepressorQuantity += GetRepressorRate() * DELTA_TIME;
           if (RepressorQuantity < 0)
               RepressorQuantity = 0;
           return nowRepressorQuantity;
       }

       function GetNextGasQuantity()
       {
           nowGasQuantity = GasQuantity;
           GasQuantity += GetGasRate() * DELTA_TIME;
           if (GasQuantity < 0)
               GasQuantity = 0;
           return nowGasQuantity ;
       }
       
       function GetNextAhlrQuantity()
       {
           nowAhlrQuantity = AhlrQuantity;
           AhlrQuantity += GetAhlrRate() * DELTA_TIME;
           if (AhlrQuantity < 0)
               AhlrQuantity = 0;
           return nowAhlrQuantity ;
       }
       
       function GetNextAhlQuantity()
       {
           nowAhlQuantity = AhlQuantity;
           AhlQuantity += GetAhlRate() * DELTA_TIME;
           if (AhlQuantity < 0)
               AhlrQuantity = 0;
           return nowAhlQuantity ;
       }
       
       function GetProteinGazRate( )
       {
         
           var result = 0;
           if (nowRepressorQuantity >= ProteinGazThreshold)
               result = ProteinGazPromoterStrength * ProteinGazSize * Math.exp( - (nowRepressorQuantity - ProteinGazThreshold) / ProteinGazTimeConstant);
           else
               result = ProteinGazPromoterStrength * ProteinGazSize;
           var halfLifeInfluence =  nowProteinGazQuantity / ProteinGazHalfLife ;
           result -= halfLifeInfluence;
           return result;
       }

       function GetAhlRate( )
       {
           var result = 0;
           if (nowRepressorQuantity >= AhlThreshold)
               result = AhlPromoterStrength * AhlSize * Math.exp( - (nowRepressorQuantity - AhlThreshold) / AhlTimeConstant);
           else
               result = AhlPromoterStrength * AhlSize;
           var halfLifeInfluence =  nowAhlQuantity / AhlHalfLife ;
           result -= halfLifeInfluence;
           return result;
       }
       
       function GetRepressorRate()
       {
           var result = 0;
           var halfLifeInfluence = nowRepressorQuantity/ ProteinGazHalfLife;

           if (nowGasQuantity < RepressorThreshold)
               result = 0;
           else
               result = RepressorPromoterStrength * RepressorSize - RepressorPromoterStrength * RepressorSize * Math.exp( - (nowGasQuantity - RepressorThreshold) / RepressorTimeConstant);
           result -= halfLifeInfluence;
           return result;
       }
       
       function GetAhlrRate()
       {
           var result = 0;
           var halfLifeInfluence = nowAhlrQuantity/ AhlrHalfLife;

           if (nowGasQuantity < AhlrThreshold)
               result = 0;
           else
               result = AhlrPromoterStrength * AhlrSize - AhlrPromoterStrength * AhlrSize * Math.exp( - (nowGasQuantity - AhlrThreshold) / AhlrTimeConstant);
           result -= halfLifeInfluence;
           return result;
       }
       
       function GetGasRate()
       {
         var result = 0;
         result += GasProductionFactor * nowProteinGazQuantity;
         result -= GasDissipation;
         return result;
       }
       

       function LoadParams( params )
       {
           //Reset values
           ProteinGazQuantity = 0;
           RepressorQuantity = 0;
           GasQuantity = 0 ;
           AhlrQuantity = 0;
           AhlQuantity = 0;
           
           nowProteinGazQuantity = 0;
           nowRepressorQuantity = 0;
           nowGasQuantity = 0 ;
           nowAhlrQuantity = 0;
           nowAhlQuantity = 0;
           
           if(params != null)
           {
           
             if(!isNaN(params['GasProteinHalfLife' ]))  ProteinGazHalfLife = params['GasProteinHalfLife' ];
             if(!isNaN(params['GasProteinStrength' ]))ProteinGazPromoterStrength = params['GasProteinStrength' ];
             if(!isNaN(params['GasProteinSize'] ))  ProteinGazSize = params['GasProteinSize'] ;
             if(!isNaN(params['GasProteinThreshold'] ))ProteinGazThreshold = params['GasProteinThreshold'] ;
             if(!isNaN(params['GasProteinSensitivity'] ))ProteinGazTimeConstant = params['GasProteinSensitivity'];
             
             if(!isNaN(params['GasProduction'] )) GasProductionFactor = params['GasProduction'];
             if(!isNaN(params['GasDiffusion' ])) GasDissipation = params['GasDiffusion' ];//woops
             
             if(!isNaN(params['RepressorHalfLife' ])) RepressorHalfLife = params['RepressorHalfLife'];
             if(!isNaN(params['RepressorStrength']))  RepressorPromoterStrength = params['RepressorStrength'];
             if(!isNaN(params['RepressorSize' ])) RepressorSize = params['RepressorSize' ];
             if(!isNaN(params['RepressorThreshold'] ))  RepressorThreshold = params['RepressorThreshold'];
             if(!isNaN(params['RepressorSensitivity'] )) RepressorTimeConstant = params['RepressorSensitivity'] ;
             
             if(!isNaN(params['AhlrHalfLife' ])) AhlrHalfLife = params['AhlrHalfLife'];
             if(!isNaN(params['AhlrStrength']))  AhlrPromoterStrength = params['AhlrStrength'];
             if(!isNaN(params['AhlrSize' ])) AhlrSize = params['AhlrSize' ];
             if(!isNaN(params['AhlrThreshold'] ))  AhlrThreshold = params['AhlrThreshold'];
             if(!isNaN(params['AhlrSensitivity'] )) AhlrTimeConstant = params['AhlrSensitivity'] ;
             
             if(!isNaN(params['AhlHalfLife' ])) AhlHalfLife = params['AhlHalfLife'];
             if(!isNaN(params['AhlStrength']))  AhlPromoterStrength = params['AhlStrength'];
             if(!isNaN(params['AhlSize' ])) AhlSize = params['AhlSize' ];
             if(!isNaN(params['AhlThreshold'] ))  AhlThreshold = params['AhlThreshold'];
             if(!isNaN(params['AhlSensitivity'] )) AhlTimeConstant = params['AhlSensitivity'] ;
             
             
             if(!isNaN(params['DeltaTime'] ))  DELTA_TIME = params['DeltaTime'];
             if(!isNaN(params['DataSize'] )) SAMPLE_POINTS = params['DataSize'];
             
           }
       }        
       
       

var g_log = new Array(); var g_minPriorityForLog = 50; function Log(message, priority) { if(priority == undefined) priority = 5; if(priority <= g_minPriorityForLog)

 {
    //console.log(message);
   g_log .push( message );
 }

}

function CreateProperMessage ( command , value ) {

   var stringed = JSON.stringify(value);
   var obs = { "command" : command, "vals" : stringed };
   var total = JSON.stringify(obs);
   return total;

}

function ReadProperMessage(message) {

   var obj = null;
   try{ obj = JSON.parse(message);}
   catch (ex) { obj = null/*postMessage("Unrecognized command") ;*/ }
   
   if(obj != null )
   {
       var v = JSON.parse(obj.vals);
       var c =  obj.command;
       obj = { "command" : c, "vals" : v };
   }
   return obj;

}

/** Shove something similar in the background process

• /

self.onmessage = function (e) {

   var obj = e.data;
   if(obj != null )
   {
       if ( obj.command == "process" )
       {
           LoadParams(obj.vals);
           var res = new Array();
           res.push(["Time","Gas Protein","Repressor","Gas","AhlR","Ahl"])
           for (var ii = 0; ii < SAMPLE_POINTS; ++ii)
           { 
               //TODO: Somehow make these calls simultaneous. They use values from the future currently.
               var pg = GetNextProteinGazQuantity();
               var rep = GetNextRepressorQuantity();
               var gas = GetNextGasQuantity();
               var ahlr = GetNextAhlrQuantity();
               var ahl = GetNextAhlQuantity();
               res.push([ii*DELTA_TIME , pg, rep, gas, ahlr,ahl]);
           }
           postMessage({"command":"process" ,"vals":res});
       }
       else if(obj.command == "graph-rep")
       {
         var REP_SAMPLES = 100;
       
         LoadParams(obj.vals);
         var res = new Array();
         res.push(["Gas","Delta Repressor"])
         for( var ii = 0; ii < REP_SAMPLES ; ++ ii)
         {
           var delta = GetRepressorRate();
           res.push([nowGasQuantity, delta]);
           nowGasQuantity += 0.5;
         }
         postMessage({"command":"graph-rep" ,"vals":res});
       }
       else if(obj.command == "graph-gas")
       {
         var GAS_SAMPLES = 100;
         var GAS_P_SAMPLES = 100;
       
         LoadParams(obj.vals);
         var total_res = [ null, null];
         var res = new Array();
         res.push(["Gas Protein","Delta Gas"])
         for( var ii = 0; ii < GAS_SAMPLES ; ++ ii)
         {
           var delta_gas = GetGasRate();
           res.push([nowProteinGazQuantity, delta_gas]);
           nowProteinGazQuantity += 0.5;
         }
         total_res[0] = res;
         LoadParams(obj.vals);
         res = new Array();
         res.push(["Repressor","Delta Gas Protein"])
         for( var ii = 0; ii < GAS_P_SAMPLES ; ++ ii)
         {
           var delta_gas = GetProteinGazRate();
           res.push([nowRepressorQuantity, delta_gas]);
           nowRepressorQuantity += 0.5;
         }
         total_res[1] = res;
         
          postMessage({"command":"graph-gas" ,"vals":total_res});
       }
       else
       {
         postMessage({'command':'error', 'vals':'Unrecognized command'});
         Log("unrecognized command received");
       }
   }

   else
   {
     postMessage({'command':'error', 'vals':'Unformatted message'});
     Log("Unformatted message received");
   }
   

};