Difference between revisions of "Team:Peking/Workplace"

 
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<div id="navigation" class="navbar navbar-fixed-top">
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            <div id="logo" style="max-width:170px"><a class="" href="https://2016.igem.org/Team:Peking"></a></div>
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            <div class="nav-collapse collapse">
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                    <li class="menu-1"><a class="colapse-menu1" href="https://2016.igem.org/Team:Peking" >Home</a></li>
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                    <li class="dropdown menu-2"><a class="dropdown-toggle" data-toggle="dropdown" href="#" > Achievements</a>
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                        <ul class="dropdown-menu">
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                            <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>
 +
                        </ul>
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                    </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>
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                            <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>
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                            <li><a href="https://2016.igem.org/Team:Peking/Clearance" >Clearance</a></li>
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                            <li><a href="https://2016.igem.org/Team:Peking/Secretion" >Secretion</a></li>
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                            <li><a href="https://2016.igem.org/Team:Peking/Proof" >Final Performance</a></li>
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                        </ul>
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                    </li>
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                    <li class="dropdown menu-4"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Modeling</a>
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                        <ul class="dropdown-menu">
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                            <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>
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                    <li class="dropdown menu-5"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Practices</a>
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                        <ul class="dropdown-menu">
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                            <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>
 +
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                    </li>
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                    <li class="menu-6"><a class="colapse-menu1" href="https://2016.igem.org/Team:Peking/Safety" >Safety</a>
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                        <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>
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                        </li>
 +
                        <li class="menu-8"><a class="colapse-menu1" href="https://2016.igem.org/Team:Peking/Interlab" >Interlab</a>
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                        </li>
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        <!-- Page Title======================================================================== -->
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        <div id="page-title">
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            <div class="row">
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                <div class="twelve columns centered text-center">
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                    <h1>Software</h1>
 +
                    <p class="title1" style="text-align:center"> Test our methods with software we designed.</p>
 +
                </div>
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        <!-- Page Title End-->
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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">
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                        <div class="row">
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                            <div class="twelve columns">
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                                <div class="texttitle">Description of SoP</div>
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 +
<div align="center" >
 +
<div style="bottom: 20px; background:#FFFFFF; color:#333333; width:80%; overflow:auto; height:300px;"  >
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<div  align="left" style="width:90%;">
 +
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<span style="font-size:20px">For the software given bellow, it was programmed based on eq (5):</span>
 +
 +
<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>
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</div>
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 +
 +
<div class="texttitle">The SoP Calculator</div>
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<div align="center">
 
<div align="center">
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<div id="barchart1" style="height:400px">The browser has blocked javascript</div>
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<div id="barchart1" style="height:400px">Loading... <br>The browser may has blocked javascript</div>
 
</div>
 
</div>
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<div align="center" >Drag to zoom in</div>
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<div align="center" class="STYLE2" style="font-size:18px; margin-bottom:18px; color:#5C9085">Drag to zoom in</div>
  
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<div align="center"><button onClick="GenerateChart()" style="font-size:18px; font:'Times New Roman', Times, serif" >Generate Chart</button>
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<div align="center"><button onClick="GenerateChart()" style="font-size:24px; font:Geneva, Arial, Helvetica, sans-serif" >Generate Chart</button>
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<button onClick="ChangeLog(this)"  style="font-size:18px; font:'Times New Roman', Times, serif" >Logarithmic Coordinate</button>
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<button onClick="ChangeLog(this)"  style="font-size:24px; font:Geneva, Arial, Helvetica, sans-serif">Logarithmic Coordinate</button>
 
</div>
 
</div>
 
<div align="center">
 
<div align="center">
 
   <table width="700" border="1" bordercolor="#4d7d75">
 
   <table width="700" border="1" bordercolor="#4d7d75">
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     <caption  >
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     <caption  style="font-size:20px;">
 
       Parameters
 
       Parameters
 
     </caption>
 
     </caption>
 
     <tr>
 
     <tr>
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       <td width="200" align="center"><table width="200" border="0">
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           <caption >
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           <caption style="font-size:20px;" >
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             Functional Group Numbers  
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             Functional Group <br/>Numbers  
 
           </caption>
 
           </caption>
 
         <tr>
 
         <tr>
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             <td  style="width:auto" nowrap="nowrap"><span  >Fa</span><br>
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             <td  style="width:auto" nowrap="nowrap"><span  style="font-size:20px;">F<sub>A</sub></span><br>
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                 <input name="fa" id="IN_fa"   onchange="UpdateData()" value="3" style="width:80px; font-size:80px; font:Arial, Helvetica, sans-serif"/>
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                 <input name="fa" id="IN_fa" style="font-size:20px; width:80px"  onchange="UpdateData()" value="3" />
 
        
 
        
 
             </td>
 
             </td>
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           <td width="100" nowrap="nowrap"><span >Fb</span><br>
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           <td width="100" nowrap="nowrap"><span style="font-size:20px;" >F<sub>B</sub></span><br>
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               <input name="fb"   id="IN_fb" onChange="UpdateData()" value="3" width="100"/>
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               <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="200" align="center"><table width="230" border="0">
 
       <td width="200" align="center"><table width="230" border="0">
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         <caption  >
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         <caption  style="font-size:20px;">
−
           Molar Concentration (mol/L)
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           Molar Concentration <br/>(mol/L)
 
           </caption>
 
           </caption>
 
         <tr>
 
         <tr>
−
           <td width="100" nowrap="nowrap"><span  >Na</span><br>
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           <td width="100" nowrap="nowrap"><span  style="font-size:20px;">N<sub>A</sub></span><br>
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               <input name="na"   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  >Nb</span><br>
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           <td width="100" nowrap="nowrap"><span  style="font-size:20px;">N<sub>B</sub></span><br>
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               <input name="nb"   id="IN_Nb" onChange="UpdateData()" value="0.214" width="100px"/>
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               <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="300" align="center"><table width="219" border="0">
 
     <td width="300" align="center"><table width="219" border="0">
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         <caption >
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         <caption style="font-size:20px;" >
 
           Monomer Weight<br />
 
           Monomer Weight<br />
−
           （kDa）
+
           (kDa)
 
         </caption>
 
         </caption>
 
         <tr>
 
         <tr>
−
           <td width="120" nowrap="nowrap"><span  >MA</span><br>
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           <td width="120" nowrap="nowrap"><span  style="font-size:20px;">M<sub>A</sub></span><br>
−
               <input name="MA" id="IN_MA"  onchange="UpdateData()" value="21.4" width="100"/>
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               <input name="MA" style="font-size:20px;  width:100px" id="IN_MA"  onchange="UpdateData()" value="21.4" />
 
   
 
   
 
             </td>
 
             </td>
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           <td width="120"><span >MB</span><br>
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           <td width="120"><span style="font-size:20px;" >M<sub>B</sub></span><br>
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             <input name="MB"   id="IN_MB" onChange="UpdateData()" value="55.4" width="100"/>
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             <input name="MB" style="font-size:20px; width:100px" id="IN_MB" onChange="UpdateData()" value="55.4" />
 
      
 
      
 
             </td>
 
             </td>
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     <tr>
 
     <tr>
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       <td width="210"><div align="center"  >Reaction Degree </div></td>
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       <td width="206"><div align="center"  style="font-size:20px;">Reaction Degree </div></td>
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       <td width="231" nowrap="nowrap"><div align="center"  >Correction Factors </div></td>
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       <td width="227" nowrap="nowrap"><div align="center"  style="font-size:20px;">Correction Factors </div></td>
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       <td width="287"><div align="center" >Calculational Range</div></td>
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       <td width="245"><div align="center" style="font-size:20px;" >Calculational Range</div></td>
 
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       <td ><table width="203" height="168" border="0">
 
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         <tr>
−
           <td width="200" height="62" nowrap="nowrap"><span  >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"   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  >Pf </span><br>
+
           <td height="36" nowrap="nowrap"><span  style="font-size:20px;">P<sub>f</sub> </span><br>
−
               <input name="pf"   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"  >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" ><span  >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 >Pa_d</span>
+
           <td nowrap="nowrap"><span style="font-size:20px;" >P<sub>a_d</sub></span>
−
               <input name="pad"  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  >Pb_d</span>
+
           <td nowrap="nowrap"><span  style="font-size:20px;">P<sub>b_d</sub></span>
−
               <input name="pbd"   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  >Weight Constraint(KDa)</span><br>
+
       <td nowrap="nowrap"><span  style="font-size:20px;">Weight Constraint(kDa)</span><br>
 
    
 
    
−
         <input name="ML"   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>
Line 116: Line 279:
 
    
 
    
 
   <p>&nbsp;</p>
 
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−
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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)