Difference between revisions of "Team:Peking/Workplace"

 
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         <title>Recovery</title>
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         <title>Home</title>
 
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         <meta name="description" content="Wiki of Peking iGEM 2016" />
 
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         <link rel="stylesheet" href="https://2016.igem.org/Template:Peking/css/priorstyle?action=raw&ctype=text/css"/>
 
         <link rel="stylesheet" href="https://2016.igem.org/Template:Peking/css/priorstyle?action=raw&ctype=text/css"/>
 
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<script language="javascript" type="text/javascript">
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<body onLoad="init()">
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function init() //确保执行一次
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−
PSET=new Pset(1,1,1,1,1);
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NSET=new Nset(1,1);
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CCa=0;
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CCb=0;
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MA=25;
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UpdateData();
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GenerateChart();
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+
<!-- Navigation -->
−
];
+
<div id="navigation" class="navbar navbar-fixed-top">
−
function factorial (n) {
+
    <div class="navbar-inner ">
−
if (n == 0 || n == 1)
+
        <div class="container no-padding">
−
return 1;
+
            <a class="show-menu" data-toggle="collapse" data-target=".nav-collapse"><span class="show-menu-bar"></span>
−
if (f[n] > 0)
+
            </a>
−
return f[n];
+
            <div id="logo" style="max-width:170px"><a class="" href="https://2016.igem.org/Team:Peking"></a></div>
−
else
+
           
−
return f[n] = factorial(n-1) * n;
+
            <div class="nav-collapse collapse">
−
}
+
                <ul class="nav">
 +
                    <li class="menu-1"><a class="colapse-menu1" href="https://2016.igem.org/Team:Peking" >Home</a></li>
 +
                    <li class="dropdown menu-2"><a class="dropdown-toggle" data-toggle="dropdown" href="#" > Achievements</a>
 +
                        <ul class="dropdown-menu">
 +
                            <li><a href="https://2016.igem.org/Team:Peking/Demonstrate" >Results</a></li>
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                            <li><a href="https://2016.igem.org/Team:Peking/Basic_Part" >Parts</a></li>
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                            <li><a href="https://2016.igem.org/Team:Peking/Collaborations" >Collaborations</a></li>
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                    <li class="dropdown menu-3"><a class="dropdown-toggle" data-toggle="dropdown" href="#">Project</a>
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                        <ul class="dropdown-menu">
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                            <li><a href="https://2016.igem.org/Team:Peking/Description" >Overview</a></li>
 +
                            <li><a href="https://2016.igem.org/Team:Peking/Design" >Design</a></li>
 +
                            <li><a href="https://2016.igem.org/Team:Peking/Crosslinking" >Crosslinking</a></li>
 +
                            <li><a href="https://2016.igem.org/Team:Peking/Uranyl-adsorption" >Uranyl adsorption</a></li>
 +
                            <li><a href="https://2016.igem.org/Team:Peking/Clearance" >Clearance</a></li>
 +
                            <li><a href="https://2016.igem.org/Team:Peking/Secretion" >Secretion</a></li>
 +
                            <li><a href="https://2016.igem.org/Team:Peking/Proof" >Final Performance</a></li>
 +
                        </ul>
 +
                    </li>
 +
                    <li class="dropdown menu-4"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Modeling</a>
 +
                        <ul class="dropdown-menu">
 +
                            <li><a href="https://2016.igem.org/Team:Peking/Model/GelPoint" > Model of Gel Point </a></li>
 +
                            <li><a href="https://2016.igem.org/Team:Peking/Model/MassDistribution" > Model of Mass Distribution</a></li>
 +
                            <li><a href="https://2016.igem.org/Team:Peking/Software" >Software</a></li>
 +
                        </ul>
 +
                    </li>
 +
                    <li class="dropdown menu-5"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Practices</a>
 +
                        <ul class="dropdown-menu">
 +
                            <li><a href="https://2016.igem.org/Team:Peking/HP/Gold" >Overview</a></li>
 +
                            <li><a href="https://2016.igem.org/Team:Peking/HP/311" >Field research</a></li>
 +
                            <li><a href="https://2016.igem.org/Team:Peking/HP/questionnaire" >Questionnaire</a></li>
 +
                            <li><a href="https://2016.igem.org/Team:Peking/HP/consulting" >Consulting</a></li>
 +
                            <li><a href="https://2016.igem.org/Team:Peking/HP/otherHP" >Education&nbsp;&amp;&nbsp;Other</a></li>
 +
                        </ul>
 +
                    </li>
 +
                    <li class="menu-6"><a class="colapse-menu1" href="https://2016.igem.org/Team:Peking/Safety" >Safety</a>
 +
                        <li class="dropdown menu-7"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Lab</a>
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                            <ul class="dropdown-menu">
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                                <li><a class="" href="https://2016.igem.org/Team:Peking/Team" >Team</a></li>
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                                <li><a class="" href="https://2016.igem.org/Team:Peking/Attributions" >Attribution</a></li>
 +
                                <li><a class="" href="https://2016.igem.org/Team:Peking/Notebook" >Notebook</a></li>
 +
                            </ul>
 +
                        </li>
 +
                        <li class="menu-8"><a class="colapse-menu1" href="https://2016.igem.org/Team:Peking/Interlab" >Interlab</a>
 +
                        </li>
 +
            </div>
 +
        </div>
 +
    </div>
 +
</div>
 +
<!--/Navigation -->
 +
       
 +
       
 +
       
 +
       
 +
        <!-- Page Title======================================================================== -->
 +
        <div id="page-title">
 +
            <div class="row">
 +
                <div class="twelve columns centered text-center">
 +
                    <h1>Software</h1>
 +
                    <p class="title1" style="text-align:center"> Test our methods with software we designed.</p>
 +
                </div>
 +
            </div>
 +
        </div>
 +
        <!-- Page Title End-->
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 +
       
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        <div class="content-outer">
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            <div id="page-content" class="row page">
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                <div id="primary" class="twelve columns">
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 +
                    <section id="overviewpic" class="content">
 +
                        <div class="row">
 +
                            <div class="twelve columns">
 +
                                <div class="texttitle">Description of SoP</div>
  
−
function num2e(num,fix){
+
<div align="center" >
−
if (num==0) return 0;
+
<div style="bottom: 20px; background:#FFFFFF; color:#333333; width:80%; overflow:auto; height:300px;"  >
−
    var p = Math.floor(Math.log(num)/Math.LN10);
+
<div  align="left" style="width:90%;">
−
    var n = num * Math.pow(10, -p);
+
−
if ((p>-2)&(p<3)) return num.toFixed(fix);     return n.toFixed(fix) + 'e' + p;
+
−
}
+
  
−
function Num(Ca,Cb,Ps,Ns) // how much mol/L of Ca,Cb
+
<span style="font-size:20px">For the software given bellow, it was programmed based on eq (5):</span>
−
{
+
−
//only a function
+
−
var Pa=Ps.Pf*0.5*(Ns.Na*Ps.fa+Ns.Nb*Ps.fb)/(Ns.Na*Ps.fa);
+
−
var Pb=Ps.Pf*0.5*(Ns.Na*Ps.fa+Ns.Nb*Ps.fb)/(Ns.Nb*Ps.fb);
+
−
var Pa1=Pa*Ps.Pa_;var Pb1=Pb*Ps.Pb_;
+
−
if (Pa1>1) Pa1=1;
+
−
if (Pb1>1) Pb1=1;
+
−
var fa=Ps.fa, fb=Ps.fb;
+
−
+
−
var Res=Ps.Pf*0.5*(Ns.Na*fa+Ns.Nb*fb)*Math.pow(Pa1,Cb-1)*Math.pow(Pb1,Ca-1)*Math.pow(1-Pa1,Ca*(fa-1)-Cb+1)*Math.pow(1-Pb1,Cb*(fb-1)-Ca+1)
+
−
*factorial(Ca*fa-Ca)*factorial(Cb*fb-Cb)/factorial(Ca*fa-Ca-Cb+1)/factorial(Cb*fb-Ca-Cb+1)/factorial(Ca)/factorial(Cb);
+
−
+
−
return Res;
+
−
}
+
  
 +
<div align="center" style="margin-bottom:10px; margin-top:10px;">
 +
<a href="https://static.igem.org/mediawiki/2016/a/a8/T--Peking--image_softwareinstruction_eq1.01.png"><img  src="https://static.igem.org/mediawiki/2016/a/a8/T--Peking--image_softwareinstruction_eq1.01.png" width="100%"></a>
 +
</div>
 +
<p> <span style="font-size:20px">Most of these parameters’ definitions can be found from <a href="https://2016.igem.org/Team:Peking/Model/MassDistribution">our introduction page</a></span><br> The “Weight Constraint” sets the confine of the molecular weight coordinate for both displaying and calculating. The “Monomer Weight”, defined as its name, may affect the height and the horizontal position of a bar in the chart. If one wish to compare the generated chart with experimental data that uses mass concentration as unit, the molar concentration must be changed according to the “Monomer Weight” as well. K<sub>d</sub>, P<sub>f</sub> and P<sub>c</sub> are automatically generated after inputting other parameters (K<sub>d </sub> and P<sub>f</sub> affect each other). Click “Generate Chart” to obtain the theoretical outcome from eq (5). Adjust P<sub>a_d</sub>, P<sub>b_d</sub> and P<sub>f</sub> according to your experimental data to find a similar point. The optimized value of P<sub>a_d</sub> and P<sub>b_d</sub> would be the indicator of hindrance or recruiting.<br></p>
  
 +
<p>
 +
<span style="font-size:20px">For example, the parameters given bellow corresponds to a reaction under the following condition:</span> <br>
 +
<strong>I</strong>. 1 mol/L of <b>3-A</b> monomers and 1mol/L of <b>3-B</b> monomers are mixed together.
 +
A <b>3-A</b> monomer has three functional groups <b>a</b> that can exclusively react with one functional group <b>b</b>.<br>
 +
  <strong>II. </strong>The molecule weight of <b>3-A</b> is 21.4kDa and the molecule weight of <b>3-B</b> is 55.4kDa. <br>
 +
  <strong>III.</strong> The column chart to be generated describes the state at "P<sub>f</sub> = 0.3" (30% of all the functional groups have reacted, and the other 70% have not).
 +
  <br>
 +
  <strong>IV.</strong> Things like non-reactive protein attached to <b>3-A</b> (or <b>3-B</b>) may have influence on the reaction between <b>a</b> and <b>b</b>. If one of a <b>3-A</b>'s functional group <b>a</b> has reacted, the other functional groups on this <b>3-A</b> will have a 1.5 times of its original chance to react. "P<sub>b_d</sub>=1" means no such effect is imposed on <b>b</b>. <br></p>
 +
<p>
 +
<span style="font-size:20px">Sometimes the following parameters also need to be cared: </span><br>
 +
<strong>I.</strong> Weight Constraint= 300 makes the horizontal coordinate ranges from 21.4 kDa (the smallest molecule weight in the system) to 300kDa.<br>
 +
<strong>II.</strong> Click "Logarithmic Coordinate/Linear Coordinate" to change the attribute of the chart's horizontal coordinate. <br>
 +
<strong>III.</strong> If the P<sub>f</sub>/P<sub>c</sub> at the left-bottom corner of the parameter panel becomes green, which means gelation, the result of the generated column chart is invalid.</p>
 +
</div>
 +
</div>
 +
</div>
  
  
−
function test()
+
<div class="texttitle">The SoP Calculator</div>
−
{
+
−
document.getElementById("OU_Pc").innerHTML=factorial(30);
+
−
}
+
  
−
function Pset(pf,pb_,pa_,fa,fb)
 
−
{
 
−
this.Pf=pf;
 
−
this.Pa_=pa_;//Pa*pa_ = Pa'
 
−
this.Pb_=pb_;
 
−
this.fa=fa;
 
−
this.fb=fb;
 
−
return this;
 
−
}
 
−
 
−
function Nset(Na,Nb)
 
−
{
 
−
this.Na=Na;
 
−
this.Nb=Nb;
 
−
return this;
 
−
}
 
−
 
−
function r1()
 
−
{
 
−
 
−
}
 
−
 
−
function UpdateData()
 
−
{
 
−
 
−
 
−
MA=parseFloat(document.getElementById("IN_MA").value);
 
−
if (MA<0) MA=0;
 
−
document.getElementById("IN_MA").value=MA.toFixed(2);
 
−
 
−
MB=parseFloat(document.getElementById("IN_MB").value);
 
−
if (MB<0) MB=0;
 
−
document.getElementById("IN_MB").value=MB.toFixed(2);
 
−
 
−
var mbig=MA;
 
−
if (MB>MA) mbig=MB;
 
−
MLimit=parseFloat(document.getElementById("IN_MLimit").value)
 
−
if (MLimit<mbig) MLimit=mbig;
 
−
if (MLimit>mbig*50) MLimit=mbig*50;
 
−
document.getElementById("IN_MLimit").value=MLimit.toFixed(2);
 
−
 
−
PSET.fa=parseInt(document.getElementById("IN_fa").value);
 
−
PSET.fb=parseInt(document.getElementById("IN_fb").value);
 
−
if (PSET.fa<1) PSET.fa=1;
 
−
if (PSET.fb<1) PSET.fb=1;
 
−
if (PSET.fa>10) PSET.fa=10;
 
−
if (PSET.fb>10) PSET.fb=10;
 
−
document.getElementById("IN_fb").value=PSET.fb;
 
−
document.getElementById("IN_fa").value=PSET.fa;
 
−
 
−
PSET.Pa_=parseFloat(document.getElementById("IN_Pa_").value);
 
−
if (PSET.Pa_<0) PSET.Pa_=0;
 
−
document.getElementById("IN_Pa_").value=num2e(PSET.Pa_,3);
 
−
 
−
PSET.Pb_=parseFloat(document.getElementById("IN_Pb_").value);
 
−
if (PSET.Pb_<0) PSET.Pb_=0;
 
−
document.getElementById("IN_Pb_").value=num2e(PSET.Pb_,3);
 
−
 
−
NSET.Na=parseFloat(document.getElementById("IN_Na").value);
 
−
if (NSET.Na<0) NSET.Na=0;
 
−
document.getElementById("IN_Na").value=num2e(NSET.Na,3);
 
−
 
−
NSET.Nb=parseFloat(document.getElementById("IN_Nb").value);
 
−
if (NSET.Nb<0) NSET.Nb=0;
 
−
document.getElementById("IN_Nb").value=num2e(NSET.Nb,3);
 
−
 
−
Kd=parseFloat(document.getElementById("IN_Kd").value);
 
−
if (Kd<0) Kd=0;
 
−
document.getElementById("IN_Kd").value=num2e(Kd,2);
 
−
 
−
 
−
/*
 
−
PSET.Pf=parseFloat(document.getElementById("IN_Pf").value);
 
−
if (PSET.Pf<0) PSET.Pf=0;
 
−
if (PSET.Pf>1) PSET.Pf=1;
 
−
*/
 
−
 
−
//you need to get Pc now
 
−
Pc=2*Math.sqrt(NSET.Na*NSET.Nb*PSET.fa*PSET.fb/(PSET.fa-1)/(PSET.fb-1))/(NSET.Na*PSET.fa+NSET.Nb*PSET.fb);
 
−
if (Pc!=NaN)
 
−
{
 
−
document.getElementById("OU_Pc").innerHTML="Pc = "+Pc.toFixed(3)+" ;";
 
−
}
 
−
else
 
−
{
 
−
document.getElementById("OU_Pc").innerHTML=" Pc = - ;";
 
−
}
 
−
// Then Pf as a out
 
−
var alfun=NSET.Na*PSET.fa+NSET.Nb*PSET.fb;
 
−
PSET.Pf=1+Kd/(alfun)-Math.sqrt((Kd+alfun)*(Kd+alfun)-4*NSET.Na*NSET.Nb*PSET.fa*PSET.fb)/alfun;
 
−
if (PSET.Pf>1) PSET.Pf=1;
 
−
document.getElementById("IN_Pf").value=num2e(PSET.Pf,3);
 
−
 
−
document.getElementById("OU_Pfc").innerHTML="Pf/Pc = "+(PSET.Pf/Pc).toFixed(3)+" ;";
 
−
if (PSET.Pf>=Pc)
 
−
    document.getElementById("OU_Pfc").style.color='#5C9085';
 
−
else
 
−
document.getElementById("OU_Pfc").style.color='#000000';
 
−
 
−
}
 
−
 
−
function UpdateData2()
 
−
{
 
−
PSET.Pf=parseFloat(document.getElementById("IN_Pf").value);
 
−
if (PSET.Pf<0) PSET.Pf=0;
 
−
if (PSET.Pf>1) PSET.Pf=1;
 
−
document.getElementById("IN_Pf").value=num2e(PSET.Pf,3);
 
−
 
−
var x=PSET.Pf*(NSET.Na*PSET.fa+NSET.Nb*PSET.fb)/2;
 
−
Kd=(NSET.Na*PSET.fa-x)*(NSET.Nb*PSET.fb-x)/x;
 
−
document.getElementById("IN_Kd").value=num2e(Kd,2);
 
−
 
−
 
−
//you need to get Pc now
 
−
Pc=2*Math.sqrt(NSET.Na*NSET.Nb*PSET.fa*PSET.fb/(PSET.fa-1)/(PSET.fb-1))/(NSET.Na*PSET.fa+NSET.Nb*PSET.fb);
 
−
if (Pc!=NaN)
 
−
{
 
−
document.getElementById("OU_Pc").innerHTML="Pc = "+Pc.toFixed(3)+" ;";
 
−
}
 
−
else
 
−
{
 
−
document.getElementById("OU_Pc").innerHTML=" Pc = - ;";
 
−
}
 
−
// Then Pf as a out
 
−
var alfun=NSET.Na*PSET.fa+NSET.Nb*PSET.fb;
 
−
PSET.Pf=1+Kd/(alfun)-Math.sqrt((Kd+alfun)*(Kd+alfun)-4*NSET.Na*NSET.Nb*PSET.fa*PSET.fb)/alfun;
 
−
if (PSET.Pf>1) PSET.Pf=1;
 
−
document.getElementById("IN_Pf").value=num2e(PSET.Pf,3);
 
−
 
−
document.getElementById("OU_Pfc").innerHTML="Pf/Pc = "+(PSET.Pf/Pc).toFixed(3)+" ;";
 
−
if (PSET.Pf>=Pc)
 
−
    document.getElementById("OU_Pfc").style.color='#5C9085';
 
−
else
 
−
document.getElementById("OU_Pfc").style.color='#000000';
 
−
}
 
−
 
−
function Cal()
 
−
{
 
−
//checkfirst
 
−
if (!isFinite(PSET.fa*PSET.fb*PSET.Pa_*PSET.Pb_*PSET.Pf*NSET.Na*NSET.Nb*CCa*CCb*MA*MB)) return;
 
−
 
−
 
−
Bars=null;
 
−
Bars=new Array();
 
−
lBars=null;
 
−
lBars=new Array();
 
−
dataready=0;
 
−
CCa=Math.floor((MLimit/MA)+1);
 
−
CCb=Math.floor((MLimit/MB)+1);
 
−
 
−
TotalMass=MA*NSET.Na+MB*NSET.Nb;
 
−
 
−
var tag=0;
 
−
for (var i=0;i<CCa;i++)
 
−
{
 
−
for (var j=0;j<CCb;j++)
 
−
{
 
−
if ((i+j)==0) {continue;}
 
−
if (i-1>(j*PSET.fb-j)) {continue;}
 
−
if (j-1>(i*PSET.fa-i)) {continue;}
 
−
if (MA*i+MB*j>MLimit) {continue;}
 
−
Bars[tag]=
 
−
[
 
−
MA*i+MB*j,
 
−
(MA*i+MB*j)*Num(i,j,PSET,NSET)/TotalMass
 
−
];
 
−
tag++;
 
−
}
 
−
}
 
−
if (MA<MB)
 
−
{
 
−
var tp=Bars[1];
 
−
Bars[1]=Bars[0];
 
−
Bars[0]=tp;
 
−
}
 
−
tag--;
 
−
A=(Bars[tag][0]-Bars[0][0])/(Math.log(Bars[tag][0])-Math.log(Bars[0][0]));
 
−
B=Bars[tag][0]-A*Math.log(Bars[tag][0]);// newpos=Alog(old)+B
 
−
 
−
tag++;
 
−
for (var i=0;i<tag;i++)
 
−
{
 
−
lBars[i]=
 
−
[
 
−
A*Math.log(Bars[i][0])+B,
 
−
Bars[i][1]
 
−
];
 
−
}
 
−
 
−
dataready=1;
 
−
}
 
−
 
−
function Draw2()
 
−
{
 
−
if (dataready==0) return;
 
−
$('#barchart1').highcharts({
 
−
        chart: {
 
−
            type: 'column',
 
−
zoomType: 'y'
 
−
        },
 
−
credits:
 
−
{
 
−
enabled:false
 
−
},
 
−
        title: {
 
−
            text: 'Theoretical Molecular Weight Distribution'
 
−
        },
 
−
 
−
        yAxis: {
 
−
title:
 
−
{
 
−
text:"Weight Fraction"
 
−
},
 
−
labels:
 
−
{
 
−
formatter:function()
 
−
{
 
−
return (this.value*100).toFixed(1)+"%";
 
−
  }
 
−
}
 
−
        },
 
−
xAxis: {
 
−
title:
 
−
{
 
−
text:"Molecular Weight(kDa)"
 
−
},
 
−
labels:
 
−
{
 
−
formatter:function()
 
−
{
 
−
return Math.exp((this.value-B)/A).toFixed(2);
 
−
  }
 
−
}
 
−
        },
 
−
        legend: {
 
−
            enabled: 0
 
−
        },
 
−
plotOptions:
 
−
{
 
−
        series: {
 
−
                color: '#5C9085'
 
−
            }
 
−
},
 
−
        tooltip:
 
−
{
 
−
shared: true,
 
−
  useHTML: true,
 
−
        formatter: function ()
 
−
  {
 
−
                return "W: "+(Math.exp((this.x-B)/A)).toFixed(2)+'<b></br>'+"D: "+this.y;
 
−
}
 
−
        },
 
−
 
−
        series: [{
 
−
            data: lBars,
 
−
pointPadding:0.3,
 
−
animation:0,
 
−
        },]
 
−
    });
 
−
}
 
−
 
−
function Draw1()
 
−
{
 
−
if (dataready==0) return;
 
−
$('#barchart1').highcharts({
 
−
        chart: {
 
−
            type: 'column',
 
−
zoomType: 'y'
 
−
        },
 
−
credits:
 
−
{
 
−
enabled:false
 
−
},
 
−
        title: {
 
−
            text: 'Theoretical Molecular Weight Distribution'
 
−
        },
 
−
 
−
        yAxis: {
 
−
title:
 
−
{
 
−
text:"Weight Fraction"
 
−
},
 
−
labels:
 
−
{
 
−
formatter:function()
 
−
{
 
−
return (this.value*100).toFixed(1)+"%";
 
−
  }
 
−
}
 
−
        },
 
−
xAxis: {
 
−
title:
 
−
{
 
−
text:"Molecular Weight(kDa)"
 
−
},
 
−
labels:
 
−
{
 
−
formatter:function()
 
−
{
 
−
return this.value;
 
−
  }
 
−
}
 
−
        },
 
−
        legend: {
 
−
            enabled: 0
 
−
        },
 
−
    plotOptions:
 
−
{
 
−
        series: {
 
−
                color: '#72AEA1'
 
−
            }
 
−
},
 
−
        tooltip:
 
−
{
 
−
shared: true,
 
−
  useHTML: true,
 
−
        formatter: function ()
 
−
  {
 
−
                return "W: "+(this.x).toFixed(2)+'<b></br>'+"D: "+this.y;
 
−
}
 
−
        },
 
−
 
 
−
        series: [{
 
−
            data: Bars,
 
−
pointPadding:0.3,
 
−
animation:0,
 
−
        },]
 
−
    });
 
−
}
 
−
 
−
function GenerateChart()
 
−
{
 
−
//var f=new Array([1,9],[3,4],[5,8]);
 
−
    if (!isFinite(PSET.fa*PSET.fb*PSET.Pa_*PSET.Pb_*PSET.Pf*NSET.Na*NSET.Nb*CCa*CCb*MA*MB)) {alert("Invalid Parameter!");return;}
 
−
Cal();
 
−
if (uselog==0)
 
−
Draw1();
 
−
else
 
−
Draw2();
 
−
}
 
−
 
−
function ChangeLog(btn)
 
−
{
 
−
if (uselog==0)
 
−
{
 
−
uselog=1;
 
−
btn.innerHTML="Linear Coordinate";
 
−
if (dataready) Draw2();
 
−
}
 
−
else
 
−
{
 
−
uselog=0;
 
−
btn.innerHTML="Logarithmic Coordinate";
 
−
if (dataready) Draw1();
 
−
}
 
−
}
 
−
</script>
 
−
</head>
 
−
 
−
<body onload="init()">
 
 
<div align="center">
 
<div align="center">
−
<div id="barchart1"></div>
+
<div id="barchart1" style="height:400px">Loading... <br>The browser may has blocked javascript</div>
 
</div>
 
</div>
−
<p align="center" class="STYLE14">Drag to zoom in
+
<div align="center" class="STYLE2" style="font-size:18px; margin-bottom:18px; color:#5C9085">Drag to zoom in</div>
−
<p align="center" class="MSTYLE_inputboxdesc">
+
−
 
+
−
<button onclick="GenerateChart()" class="MSTYLE_inputboxdesc">Generate Chart</button>
+
−
  
+
−
<button onclick="ChangeLog(this)" class="MSTYLE_inputboxdesc">Logarithmic Coordinate</button>
+
  
 +
<div align="center"><button onClick="GenerateChart()" style="font-size:24px; font:Geneva, Arial, Helvetica, sans-serif" >Generate Chart</button>
 +
 
 +
<button onClick="ChangeLog(this)"  style="font-size:24px; font:Geneva, Arial, Helvetica, sans-serif">Logarithmic Coordinate</button>
 +
</div>
 
<div align="center">
 
<div align="center">
−
   <table width="692" border="1" bordercolor="#4d7d75">
+
   <table width="700" border="1" bordercolor="#4d7d75">
−
     <caption class="MSTYLE_inputboxdesc">
+
     <caption style="font-size:20px;">
 
       Parameters
 
       Parameters
 
     </caption>
 
     </caption>
 
     <tr>
 
     <tr>
−
       <td width="210" align="center"><table width="200" border="0">
+
       <td width="200" align="center"><table width="200" border="0">
−
           <caption class="MSTYLE_inputboxdesc">
+
           <caption style="font-size:20px;" >
−
             Functional Group Numbers  
+
             Functional Group <br/>Numbers  
 
           </caption>
 
           </caption>
 
         <tr>
 
         <tr>
−
             <td width="100" nowrap="nowrap"><span class="MSTYLE_inputboxdesc">Fa</span><br>
+
             <td style="width:auto" nowrap="nowrap"><span style="font-size:20px;">F<sub>A</sub></span><br>
−
                 <input name="fa" id="IN_fa" class="MSTYLE_inputbox" onchange="UpdateData()" value="3" width="100"/>
+
                 <input name="fa" id="IN_fa" style="font-size:20px; width:80px" onchange="UpdateData()" value="3" />
 
        
 
        
 
             </td>
 
             </td>
−
           <td width="100" nowrap="nowrap"><span class="MSTYLE_inputboxdesc">Fb</span><br>
+
           <td width="100" nowrap="nowrap"><span style="font-size:20px;" >F<sub>B</sub></span><br>
−
               <input name="fb" class="MSTYLE_inputbox" id="IN_fb" onchange="UpdateData()" value="3" width="100"/>
+
               <input name="fb" style="font-size:20px; width:80px" id="IN_fb" onChange="UpdateData()" value="3"/>
 
             </td>
 
             </td>
 
         </tr>
 
         </tr>
 
       </table></td>
 
       </table></td>
−
       <td width="230" align="center"><table width="230" border="0">
+
       <td width="200" align="center"><table width="230" border="0">
−
         <caption class="MSTYLE_inputboxdesc">
+
         <caption style="font-size:20px;">
−
           Molar Concentration (mol/L)
+
           Molar Concentration <br/>(mol/L)
 
           </caption>
 
           </caption>
 
         <tr>
 
         <tr>
−
           <td width="100" nowrap="nowrap"><span class="MSTYLE_inputboxdesc">Na</span><br>
+
           <td width="100" nowrap="nowrap"><span style="font-size:20px;">N<sub>A</sub></span><br>
−
               <input name="na" class="MSTYLE_inputbox" id="IN_Na" onchange="UpdateData()" value="0.554" width="100px"/>
+
               <input name="na" style="font-size:20px; width:120px" id="IN_Na" onChange="UpdateData()" value="1.000"/>
 
  </td>
 
  </td>
−
           <td width="100" nowrap="nowrap"><span class="MSTYLE_inputboxdesc">Nb</span><br>
+
           <td width="100" nowrap="nowrap"><span style="font-size:20px;">N<sub>B</sub></span><br>
−
               <input name="nb" class="MSTYLE_inputbox" id="IN_Nb" onchange="UpdateData()" value="0.214" width="100px"/>
+
               <input name="nb" style="font-size:20px; width:120px" id="IN_Nb" onChange="UpdateData()" value="1.000" />
 
           </td>
 
           </td>
 
         </tr>
 
         </tr>
 
       </table></td>
 
       </table></td>
−
     <td width="330" align="center"><table width="219" border="0">
+
     <td width="300" align="center"><table width="219" border="0">
−
         <caption class="MSTYLE_inputboxdesc">
+
         <caption style="font-size:20px;" >
 
           Monomer Weight<br />
 
           Monomer Weight<br />
−
           （kDa）
+
           (kDa)
 
         </caption>
 
         </caption>
 
         <tr>
 
         <tr>
−
           <td width="120" nowrap="nowrap"><span class="MSTYLE_inputboxdesc">MA</span><br>
+
           <td width="120" nowrap="nowrap"><span style="font-size:20px;">M<sub>A</sub></span><br>
−
               <input name="MA" id="IN_MA" class="MSTYLE_inputbox" onchange="UpdateData()" value="21.4" width="100"/>
+
               <input name="MA" style="font-size:20px;  width:100px" id="IN_MA"   onchange="UpdateData()" value="21.4" />
 
   
 
   
 
             </td>
 
             </td>
−
           <td width="120"><span class="MSTYLE_inputboxdesc">MB</span><br>
+
           <td width="120"><span style="font-size:20px;" >M<sub>B</sub></span><br>
−
             <input name="MB" class="MSTYLE_inputbox" id="IN_MB" onchange="UpdateData()" value="55.4" width="100"/>
+
             <input name="MB" style="font-size:20px; width:100px" id="IN_MB" onChange="UpdateData()" value="55.4" />
 
      
 
      
 
             </td>
 
             </td>
Line 526: Line 239:
 
     </tr>
 
     </tr>
 
   </table>
 
   </table>
−
   <table width="780" border="1" bordercolor="#4d7d75">
+
   <table width="700" border="1" bordercolor="#4d7d75">
 
     <tr>
 
     <tr>
−
       <td width="210"><div align="center" class="MSTYLE_inputboxdesc">Reaction Degree </div></td>
+
       <td width="206"><div align="center" style="font-size:20px;">Reaction Degree </div></td>
−
       <td width="231" nowrap="nowrap"><div align="center" class="MSTYLE_inputboxdesc">Correction Factors </div></td>
+
       <td width="227" nowrap="nowrap"><div align="center" style="font-size:20px;">Correction Factors </div></td>
−
       <td width="287"><div align="center" class="MSTYLE_inputboxdesc">Calculational Range</div></td>
+
       <td width="245"><div align="center" style="font-size:20px;" >Calculational Range</div></td>
 
     </tr>
 
     </tr>
 
     <tr>
 
     <tr>
−
       <td width="210"><table width="203" height="168" border="0">
+
       <td ><table width="203" height="168" border="0">
 
         <tr>
 
         <tr>
−
           <td width="200" height="62" nowrap="nowrap"><span class="MSTYLE_inputboxdesc">Kd(mol/L)</span><br>
+
           <td height="62" nowrap="nowrap"><span style="font-size:20px;">K<sub>d</sub>(mol/L)</span><br>
−
             <input name="kd" class="MSTYLE_inputbox" id="IN_Kd" onchange="UpdateData()" value="2.56" width="100"/></td>
+
             <input name="kd" style="font-size:20px;  width:100px" id="IN_Kd" onChange="UpdateData()" value="4.90" /></td>
 
         </tr>
 
         </tr>
 
         <tr>
 
         <tr>
−
           <td width="200" height="36" nowrap="nowrap"><span class="MSTYLE_inputboxdesc">Pf </span><br>
+
           <td height="36" nowrap="nowrap"><span style="font-size:20px;">P<sub>f</sub> </span><br>
−
               <input name="pf" class="MSTYLE_inputbox" id="IN_Pf" onchange="UpdateData2()" value="0.3" width="100"/></td>
+
               <input name="pf" style="font-size:20px;  width:100px" id="IN_Pf" onChange="UpdateData2()" value="0.3" /></td>
 
         </tr>
 
         </tr>
 
         <tr>
 
         <tr>
−
           <td width="200" height="30"><span id="OU_Pc" class="MSTYLE_inputboxdesc">Pc = &nbsp;&nbsp; ;</span><br>
+
           <td height="30"><span id="OU_Pc" style="font-size:20px;">P<sub>c</sub> = &nbsp;&nbsp; ;</span><br>
−
             <span id="OU_Pfc" class="MSTYLE_inputboxdesc"><span class="MSTYLE_inputboxdesc">Pf/Pc = </span></span></td>
+
             <span id="OU_Pfc" style="font-size:20px;" ><span style="font-size:20px;">P<sub>f</sub>/P<sub>c</sub> = </span></span></td>
 
         </tr>
 
         </tr>
 
       </table></td>
 
       </table></td>
−
       <td width="231"><table width="145" height="159" border="0">
+
       <td ><table width="145" height="159" border="0">
 
         <tr>
 
         <tr>
−
           <td width="150" nowrap="nowrap"><span class="MSTYLE_inputboxdesc">Pa_d</span>
+
           <td nowrap="nowrap"><span style="font-size:20px;" >P<sub>a_d</sub></span>
−
               <input name="pad" class="MSTYLE_inputbox" id="IN_Pa_" onchange="UpdateData()" value="1.000" width="80"/></td>
+
               <input name="pad" style="font-size:20px;  width:100px"   id="IN_Pa_" onChange="UpdateData()" value="1.500" /></td>
 
         </tr>
 
         </tr>
 
         <tr>
 
         <tr>
−
           <td width="150" nowrap="nowrap"><span class="MSTYLE_inputboxdesc">Pb_d</span>
+
           <td nowrap="nowrap"><span style="font-size:20px;">P<sub>b_d</sub></span>
−
               <input name="pbd" class="MSTYLE_inputbox" id="IN_Pb_" onchange="UpdateData()" value="1.000" width="80"/></td>
+
               <input name="pbd" style="font-size:20px;  width:100px" id="IN_Pb_" onChange="UpdateData()" value="1.000" /></td>
 
         </tr>
 
         </tr>
 
          
 
          
 
       </table></td>
 
       </table></td>
−
       <td width="287" nowrap="nowrap"><span class="MSTYLE_inputboxdesc">Weight Constraint(KDa)</span><br>
+
       <td nowrap="nowrap"><span style="font-size:20px;">Weight Constraint(kDa)</span><br>
 
    
 
    
−
         <input name="ML" class="MSTYLE_inputbox" id="IN_MLimit" onchange="UpdateData()" value="300" width="100"/>
+
         <input name="ML" style="font-size:20px;  width:150px" id="IN_MLimit" onChange="UpdateData()" value="300" />
 
   </td>
 
   </td>
 
     </tr>
 
     </tr>
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Latest revision as of 15:23, 19 October 2016

Home

Software

Test our methods with software we designed.

Description of SoP
For the software given bellow, it was programmed based on eq (5):

Most of these parameters’ definitions can be found from our introduction page
The “Weight Constraint” sets the confine of the molecular weight coordinate for both displaying and calculating. The “Monomer Weight”, defined as its name, may affect the height and the horizontal position of a bar in the chart. If one wish to compare the generated chart with experimental data that uses mass concentration as unit, the molar concentration must be changed according to the “Monomer Weight” as well. Kd, Pf and Pc are automatically generated after inputting other parameters (Kd and Pf affect each other). Click “Generate Chart” to obtain the theoretical outcome from eq (5). Adjust Pa_d, Pb_d and Pf according to your experimental data to find a similar point. The optimized value of Pa_d and Pb_d would be the indicator of hindrance or recruiting.

For example, the parameters given bellow corresponds to a reaction under the following condition:
I. 1 mol/L of 3-A monomers and 1mol/L of 3-B monomers are mixed together. A 3-A monomer has three functional groups a that can exclusively react with one functional group b.
II. The molecule weight of 3-A is 21.4kDa and the molecule weight of 3-B is 55.4kDa.
III. The column chart to be generated describes the state at "Pf = 0.3" (30% of all the functional groups have reacted, and the other 70% have not).
IV. Things like non-reactive protein attached to 3-A (or 3-B) may have influence on the reaction between a and b. If one of a 3-A's functional group a has reacted, the other functional groups on this 3-A will have a 1.5 times of its original chance to react. "Pb_d=1" means no such effect is imposed on b.

Sometimes the following parameters also need to be cared:
I. Weight Constraint= 300 makes the horizontal coordinate ranges from 21.4 kDa (the smallest molecule weight in the system) to 300kDa.
II. Click "Logarithmic Coordinate/Linear Coordinate" to change the attribute of the chart's horizontal coordinate.
III. If the Pf/Pc at the left-bottom corner of the parameter panel becomes green, which means gelation, the result of the generated column chart is invalid.

The SoP Calculator
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Parameters
Functional Group
Numbers
FA
 FB
Molar Concentration
(mol/L)
NA
 NB
Monomer Weight
(kDa)
MA
 MB
Reaction Degree
Correction Factors
Calculational Range
Kd(mol/L)
Pf
Pc =    ;
Pf/Pc =
Pa_d
Pb_d
Weight Constraint(kDa)