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Team:Concordia/Modeling/background
From 2013.igem.org
Revision as of 15:11, 27 September 2013 by Verybadalloc (Talk | contribs)
/** 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");
}
};
