Difference between revisions of "Team:NEFU China/Software1"

 
(32 intermediate revisions by 6 users not shown)
Line 5: Line 5:
 
<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1">
 
<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1">
 
<link href="https://2018.igem.org/wiki/index.php?title=Template:NEFU_China/CSS-menu&action=raw&ctype=text/css"  rel="stylesheet" type="text/css">
 
<link href="https://2018.igem.org/wiki/index.php?title=Template:NEFU_China/CSS-menu&action=raw&ctype=text/css"  rel="stylesheet" type="text/css">
−
<link href="https://2018.igem.org/wiki/index.php?title=Template:NEFU_China/CSS-members-foot&action=raw&ctype=text/css"  rel="stylesheet" type="text/css">
 
 
<link href="https://2018.igem.org/wiki/index.php?title=Template:NEFU_China/CSS-software1&action=raw&ctype=text/css"  rel="stylesheet" type="text/css">
 
<link href="https://2018.igem.org/wiki/index.php?title=Template:NEFU_China/CSS-software1&action=raw&ctype=text/css"  rel="stylesheet" type="text/css">
  
Line 19: Line 18:
 
     margin-top: 0px;
 
     margin-top: 0px;
 
     margin-left: 0px;
 
     margin-left: 0px;
 +
 
 
}
 
}
 
#menu li ul li:hover ul{
 
#menu li ul li:hover ul{
Line 112: Line 112:
 
z-index: -2;
 
z-index: -2;
 
position: absolute;
 
position: absolute;
−
margin-top: 36px!important;
+
margin-top: 0px!important;
 +
}
 +
#foot-title h3{
 +
font-size: 18px!important;
 
}
 
}
 
</style>
 
</style>
Line 122: Line 125:
 
<div id="menu" style="background-color:rgba(0,0,0,0.6)!important">
 
<div id="menu" style="background-color:rgba(0,0,0,0.6)!important">
 
<li id="nav" style="left: 8%!important; width: 100%!important;">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;
 
<li id="nav" style="left: 8%!important; width: 100%!important;">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;
−
<!--<a class="menu1" href="#" style="text-align: right;">☰</a>-->
+
 
<ul class="firstmenu" style="float: left">
 
<ul class="firstmenu" style="float: left">
 
 
Line 133: Line 136:
 
<ul id="sub_02">
 
<ul id="sub_02">
 
<li><a href="https://2018.igem.org/Team:NEFU_China/Background" target="_self">BACKGROUND</a></li>
 
<li><a href="https://2018.igem.org/Team:NEFU_China/Background" target="_self">BACKGROUND</a></li>
−
<li><a href="https://2018.igem.org/Team:NEFU_China/Description" target="_self">DESCRIPTION</a></li>
+
<li><a href="https://2018.igem.org/Team:NEFU_China/Description" target="_self">DESCRIPTION &amp; DESIGN</a></li>
−
<li><a href="https://2018.igem.org/Team:NEFU_China/Design" target="_self">DESIGN</a></li>
+
<li><a href="https://2018.igem.org/Team:NEFU_China/Coding book" target="_self">CODE BOOK</a></li>
−
<li><a href="https://2018.igem.org/Team:NEFU_China/Coding book" target="_self">CODING BOOK</a></li>
+
 
  </ul>
 
  </ul>
 
  </li>
 
  </li>
−
 
−
 
 
<li class="mainlevel" id="mainlevel_03">
 
<li class="mainlevel" id="mainlevel_03">
−
  <a href="https://2018.igem.org/Team:NEFU_China/Experiment"><img id="parts" src="https://static.igem.org/mediawiki/2018/6/62/T--NEFU_China--_RESULTS.png">EXPERIMENT</a>
+
  <a href="https://2018.igem.org/Team:NEFU_China/Demonstrate"><img id="parts" src="https://static.igem.org/mediawiki/2018/6/62/T--NEFU_China--_RESULTS.png">EXPERIMENTS</a>
 
  <ul id="sub_03">
 
  <ul id="sub_03">
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Lock_Key" target="_self">LOCK &amp; KEY</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Lock_Key" target="_self">LOCK &amp; KEY</a></li>
−
  <li><a href="https://2018.igem.org/Team:NEFU_China/Suicide" target="_self">SUICIDE</a></li>
+
  <li><a href="https://2018.igem.org/Team:NEFU_China/Suicide" target="_self">INFORMATION DESTRUCTION</a></li>
−
  <li><a href="https://2018.igem.org/Team:NEFU_China/Splicing" target="_self">SPLICING</a></li>
+
  <li><a href="https://2018.igem.org/Team:NEFU_China/Splicing" target="_self">Pre-RNA SPLICING</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Demonstrate" target="_self">DEMONSTRATE</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Demonstrate" target="_self">DEMONSTRATE</a></li>
 
  <hr>
 
  <hr>
Line 162: Line 162:
 
  <ul id="sub_05">
 
  <ul id="sub_05">
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Model" target="_self">OVERVIEW</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Model" target="_self">OVERVIEW</a></li>
−
  <li><a href="https://2018.igem.org/Team:NEFU_China/Model1" target="_self">MODEL1</a></li>
+
  <li><a href="https://2018.igem.org/Team:NEFU_China/Model1" target="_self">CORRESPONDING COEFFICIENT</a></li>
−
  <li><a href="https://2018.igem.org/Team:NEFU_China/Model2" target="_self">MODEL2</a></li>
+
  <li><a href="https://2018.igem.org/Team:NEFU_China/Model2" target="_self">KILLING MODEL</a></li>
 
  </ul>
 
  </ul>
 
  </li>
 
  </li>
Line 180: Line 180:
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Attributions" target="_self">ATTRIBUTIONS</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Attributions" target="_self">ATTRIBUTIONS</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Members" target="_self">MEMBERS</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Members" target="_self">MEMBERS</a></li>
−
 
−
  <li><a href="https://2018.igem.org/Team:NEFU_China/Sponsoring" target="_self">SPONSORING</a></li>
 
 
  </ul>
 
  </ul>
 
  </li>
 
  </li>
Line 187: Line 185:
 
  <a href="https://2018.igem.org/Team:NEFU_China/Human_Practices"><img id="humanpractice" src="https://static.igem.org/mediawiki/2018/9/91/T--NEFU_China--_HUMANPRACTICE.png">HUMAN PRACTICE</a>
 
  <a href="https://2018.igem.org/Team:NEFU_China/Human_Practices"><img id="humanpractice" src="https://static.igem.org/mediawiki/2018/9/91/T--NEFU_China--_HUMANPRACTICE.png">HUMAN PRACTICE</a>
 
  <ul id="sub_08">
 
  <ul id="sub_08">
 +
  <li><a href="https://2018.igem.org/Team:NEFU_China/Human_Practices" target="_self">OVERVIEW</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Gold_integrated" target="_self">GOLD INTEGRATED</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Gold_integrated" target="_self">GOLD INTEGRATED</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Silver" target="_self">SILVER</a></li>
 
  <li><a href="https://2018.igem.org/Team:NEFU_China/Silver" target="_self">SILVER</a></li>
Line 207: Line 206:
 
var context =canvas.getContext("2d");
 
var context =canvas.getContext("2d");
 
var W = window.innerWidth;
 
var W = window.innerWidth;
−
                         var H = 1800;
+
                         var H = 8000;
 
//var H = window.innerHeight*1.5;
 
//var H = window.innerHeight*1.5;
 
canvas.width = W;
 
canvas.width = W;
Line 273: Line 272:
 
     <div class="row banner">
 
     <div class="row banner">
 
         <div class="banner-text">
 
         <div class="banner-text">
−
             <h1 class="responsive-headline">Software 1's Name</h1>
+
             <h1 class="responsive-headline" style="color: orange!important;">Build Coding Book</h1>
−
             <h3>Software's introduction.<br>
+
             <h3 style="font-size: 25px!important;">Find out the correspondence between letters and codons.<br>
 
             </h3>
 
             </h3>
 
             <hr/>
 
             <hr/>
Line 282: Line 281:
  
 
<section id="resume" style="box-shadow: inset 0px 15px 15px -15px green">
 
<section id="resume" style="box-shadow: inset 0px 15px 15px -15px green">
−
<div class="row introduction" >
+
<div class="row introduction">
 
<div class="three columns header-col">
 
<div class="three columns header-col">
−
             <h1><span>intorduction</span></h1>
+
             <h1><span style="
 +
                color: orange;
 +
                font-size: 25px;
 +
                ">introduce</span></h1>
 
         </div>
 
         </div>
 
         <div class="nine columns main-col">
 
         <div class="nine columns main-col">
 
             <div class="row item">
 
             <div class="row item">
 
<div class="twelve columns">
 
<div class="twelve columns">
−
<h3>Aim</h3>
+
<h3 style="font-size: 45px;">Aim</h3>
 
<p class="info">Build Coding Book</p>
 
<p class="info">Build Coding Book</p>
−
<p>
+
<p style="font-size: 26px!important;">
−
In English text, each letter has a certain frequency. We constructed a list of letter frequencies for each letter. Also, in living organisms, each codon is used with a certain frequency. Based on this relationship between English letters and codons,  we find out the correspondence between letters and codons by using DFS(Depth First Search) algorithm and optimization arithmetic.
+
In English text, each letter has a certain frequency. We constructed a list of letter frequencies for each letter. Also, in living organisms, each codon is used with a certain frequency. Based on this relationship between English letters and codons,  we find out the correspondence between letters and codons by using DFS (Depth First Search) algorithm and optimization arithmetic.
 
</p>
 
</p>
 
</div>
 
</div>
Line 299: Line 301:
 
               <div class="twelve columns">
 
               <div class="twelve columns">
 
  <h3>Programming</h3>
 
  <h3>Programming</h3>
−
  <p>
+
      <br>
−
      1.Create a letter-frequency table and a codon-frequency table.<br>
+
  <p style="font-size: 26px!important;">
 +
      <strong>1. Create a letter-frequency table and a codon-frequency table.</strong><br>
 
  According to the literature, we obtain the information of the frequency of letters and codons.
 
  According to the literature, we obtain the information of the frequency of letters and codons.
−
  <br>
+
  <br><br>
−
  2.Find out the correspondence between letters and codons by using DFS Algorithm.<br>
+
  <strong>2. Find out the correspondence between letters and codons by using DFS Algorithm.</strong><br>
−
  We build up a tree structure where the codons and the frequency of the codons are stored on each node. Then we use the depth-first search algorithm to traverse down from the root node successively, and match condon-frequence with the letter- frequency to obtain the correspondence between letters and codons.<br>
+
  We build up a tree structure where the codons and the frequency of the codons are stored on each node. Then we use the depth-first search algorithm to traverse down from the root node successively, and match condon-frequence with the letter- frequency to obtain the correspondence between letters and codons.
 +
                      <br><br>
 
                       The tree structure is shown in the figure 1.<br>
 
                       The tree structure is shown in the figure 1.<br>
−
  3.Get the optimal solution by using optional algorithm.<br>
+
  <div align="center">
−
  In step 2, we get the correspondence between letters and codons. But some letters have multiple corresponding relationships. For example, in figure 1, the letters E and T correspond to codons GAU, GCU, GAA, E and T also correspond to codons GAU, GCU, AUG. What’s more, the letter T can also correspond to codons GAU, GCU, GCA. Therefore, we use the optimal algorithm to determine one of the multiple correspondence. <br>   
+
  <img style="width:750px;" src="https://static.igem.org/mediawiki/2018/b/bd/T--NEFU_China--software1-tree.png"><br>
 +
  </div>
 +
      <p>Figure 1. Tree Structute.</p>
 +
      <br><br>
 +
  <p style="font-size: 26px!important;">
 +
 
 +
                      <strong>3. Get the optimal solution by using optional algorithm.</strong></p>
 +
      <p>
 +
  In step 2, we get the correspondence between letters and codons. But some letters have multiple corresponding relationships. For example, in figure 1, the letters E and T correspond to codons GAU, GCU, GAA, E and T also correspond to codons GAU, GCU, AUG. What’s more, the letter T can also correspond to codons GAU, GCU, GCA. Therefore, we use the optimal algorithm to determine one of the multiple correspondence. <br> </p>
 +
  <!--
 +
      <table>
 +
  <tr>
 +
  <th>
 +
  Letter
 +
      </th>
 +
  <th>
 +
  Freq
 +
      </th>
 +
  </tr>
 +
  <tr>
 +
  <th>
 +
  E
 +
      </th>
 +
  <th>
 +
  12.02
 +
      </th>
 +
  </tr>
 +
  <tr>
 +
  <th>
 +
  T
 +
      </th>
 +
  <th>
 +
  9.10
 +
      </th>
 +
  </tr>
 +
      </table>
 +
      |12.02-10.53|=1.49 <br>
 +
                      |  9.10-10.53|=1.43  optimal<br>
 +
                      then:GAU,GCU,GAA—&gt;T<br>
 +
                      |12.02-10.43|=1.38  <br>
 +
                      |  9.10-10.42|=1.32&lt;1.43  optimal<br>
 +
                      then:GAU,GCU,AUG—&gt;T<br>
 +
                      |  9.10-10.39|=1.29&lt;1.32  optimal<br>
 +
                      then:GAU,GCU,GCA—&gt;T<br>-->
 
  </p>
 
  </p>
 
                 </div>
 
                 </div>
Line 317: Line 364:
 
       <div class="row results">
 
       <div class="row results">
 
         <div class="three columns header-col">
 
         <div class="three columns header-col">
−
             <h1><span>RESULTS</span></h1>
+
             <h1><span style="
 +
color: orange;
 +
font-size: 25px;
 +
">RESULTS</span></h1>
 
         </div>
 
         </div>
 
         <div class="nine columns main-col">
 
         <div class="nine columns main-col">
Line 323: Line 373:
 
               <div class="twelve columns">
 
               <div class="twelve columns">
 
               <h3>Print the correspondence between letters and codons</h3>
 
               <h3>Print the correspondence between letters and codons</h3>
−
                   <p>
+
                   <p style="
−
                  It was the best of times, it was the worst of times, it was the age of wisdom, it was the age of foolishness, it was the epoch of belief, it was the epoch of incredulity, it was the season of Light, it was the season of Darkness, it was the spring of hope, it was the winter of despair, we had everything before us, we had nothing before us, we were all going direct to Heaven, we were all going direct the other way.
+
padding-top: 20px;
−
                  </p>
+
font-size: 26px!important;
 +
">
 +
Output:<br>
 +
<br>
 +
<img src="https://static.igem.org/mediawiki/2018/2/25/T--NEFU_China--codebook_table.png">
 +
 
 +
            </p>
 
               </div>
 
               </div>
 
             </div>  
 
             </div>  
Line 333: Line 389:
 
                  
 
                  
 
                   <p>
 
                   <p>
−
                   It was the best of times, it was the worst of times, it was the age of wisdom, it was the age of foolishness, it was the epoch of belief, it was the epoch of incredulity, it was the season of Light, it was the season of Darkness, it was the spring of hope, it was the winter of despair, we had everything before us, we had nothing before us, we were all going direct to Heaven, we were all going direct the other way.
+
                    
 +
  <img style="width:750px;" src="https://static.igem.org/mediawiki/2018/4/48/T--NEFU_China--histogram.png">
 
                 </p>
 
                 </p>
 
               </div>
 
               </div>
Line 344: Line 401:
 
  <div class="row others">
 
  <div class="row others">
 
         <div class="three columns header-col">
 
         <div class="three columns header-col">
−
             <h1><span>Others</span></h1>
+
             <h1><span style="
 +
color: orange;
 +
font-size: 25px;
 +
">Others</span></h1>
 
         </div>
 
         </div>
−
         <div class="nine columns main-col">
+
         <div class="nine columns main-col" style="
 +
font-size: 26px!important;
 +
">
 
             <div class="row item">
 
             <div class="row item">
 
               <div class="twelve columns">
 
               <div class="twelve columns">
 
               <h3>Visual Software</h3>
 
               <h3>Visual Software</h3>
 
                  
 
                  
−
                   <p>
+
                   <p style="
 +
font-size: 26px!important;
 +
">
 
                   We developed a visual software. There are an input textbox, an output textbox, two radio buttons and a translate button in the software interface. We can choose radio buttons to select letters to codons or codons to letters. In addition to these, our software can also provide open files, copy files, cut files, save files, print files and other basic functions.<br>
 
                   We developed a visual software. There are an input textbox, an output textbox, two radio buttons and a translate button in the software interface. We can choose radio buttons to select letters to codons or codons to letters. In addition to these, our software can also provide open files, copy files, cut files, save files, print files and other basic functions.<br>
 
      Software interface:<br>
 
      Software interface:<br>
 +
      <br>
 +
  <div align="center">
 +
  <img style="width:750px;" src="https://static.igem.org/mediawiki/2018/5/5c/T--NEFU_China--software-v1.png"><br>
 +
  </div>
 +
  <br>
 +
 
      Letters to Codons:<br>
 
      Letters to Codons:<br>
 +
  <div align="center">
 +
  <img style="width:750px;" src="https://static.igem.org/mediawiki/2018/3/35/T--NEFU_China--software-v2.png">
 +
  </div><br>
 +
 
  Codons to letters:<br>
 
  Codons to letters:<br>
−
   
+
  <div align="center">
 +
      <img style="width:750px;" src="https://static.igem.org/mediawiki/2018/8/8d/T--NEFU_China--software-v3.png">
 +
  </div>
 
                   </p>
 
                   </p>
 
               </div>
 
               </div>
Line 375: Line 451:
 
       </div>  
 
       </div>  
 
</section>
 
</section>
−
<div class="foot">
 
−
<div id="foot-title">
 
−
<table>
 
−
<tr>
 
−
<td>
 
−
<h1>Userfull links</h1>
 
−
<h2>
 
−
<a href="https://2018.igem.org/Team:NEFU_China">Home</a>
 
−
&nbsp;&nbsp;&nbsp;
 
−
<a href="https://2018.igem.org/Team:NEFU_China/Model">Model</a>
 
−
                        &nbsp;&nbsp;
 
−
                        <a href="https://2018.igem.org/Team:NEFU_China/Description">Project</a>
 
−
&nbsp;&nbsp;
 
−
<a href="https://2018.igem.org/Team:NEFU_China/Software">Software</a>
 
−
    &nbsp;&nbsp;
 
−
    </h2>
 
−
 
−
<h2>
 
−
<a href="https://2018.igem.org/Team:NEFU_China/Basic_Part">Parts</a>
 
−
&nbsp;&nbsp;&nbsp;&nbsp;
 
−
<a href="https://2018.igem.org/Team:NEFU_China/Members">Teams</a>
 
−
&nbsp;
 
−
<a href="https://2018.igem.org/Team:NEFU_China/Lock_Key">Results</a>
 
−
&nbsp;
 
−
<a href="https://2018.igem.org/Team:NEFU_China/Notebook">Notebook</a>
 
−
                        &nbsp;&nbsp;
 
−
</h2>
 
−
 
−
<h2>
 
−
<a href="https://2018.igem.org/Team:NEFU_China/Human_Practices">Human &nbsp;Practice</a>
 
−
</h2>
 
−
</td>
 
−
<td style="padding-left: 70px">
 
−
<h1>Follow us</h1>
 
−
<img alt="facebook" src="https://static.igem.org/mediawiki/2018/b/b5/T--NEFU_China--facebook.png">
 
−
&nbsp;&nbsp;&nbsp;
 
−
        <img alt="twitter" src="https://static.igem.org/mediawiki/2018/3/36/T--NEFU_China--twitter.png">
 
−
&nbsp;&nbsp;&nbsp;
 
−
<img alt="wehchat" src="https://static.igem.org/mediawiki/2018/c/ca/T--NEFU_China--wechat.png">
 
−
        <br>
 
−
        <img alt="facebook" src="https://static.igem.org/mediawiki/2018/b/b5/T--NEFU_China--facebook.png">
 
−
&nbsp;&nbsp;&nbsp;
 
−
        <img alt="twitter" src="https://static.igem.org/mediawiki/2018/3/36/T--NEFU_China--twitter.png">
 
−
&nbsp;&nbsp;&nbsp;
 
−
<img alt="wehchat" src="https://static.igem.org/mediawiki/2018/c/ca/T--NEFU_China--wechat.png">
 
−
 
−
</td>
 
−
<td style="padding-left: 70px">
 
−
<h1>Contact us</h1>
 
−
<h3>iGEM-NEFU_China2018</h3>
 
−
<h3>Email: hexinglu@nefu.edu.cn</h3>
 
−
<h3>No.26 Hexing Road, Xiangfang <br>District, Harbin, Heilongjiang <br>Province 150000</h3>
 
−
</td>
 
−
</tr>
 
−
</table>
 
−
</div>
 
−
<div id="foot-declare">
 
−
<p>
 
−
 
−
</p>
 
−
</div>
 
−
</div>
 
 
</body>
 
</body>
  
 
</html>
 
</html>

Latest revision as of 12:55, 9 November 2018

Software 1

introduce

Aim

Build Coding Book

In English text, each letter has a certain frequency. We constructed a list of letter frequencies for each letter. Also, in living organisms, each codon is used with a certain frequency. Based on this relationship between English letters and codons, we find out the correspondence between letters and codons by using DFS (Depth First Search) algorithm and optimization arithmetic.

Programming


1. Create a letter-frequency table and a codon-frequency table.
According to the literature, we obtain the information of the frequency of letters and codons.

2. Find out the correspondence between letters and codons by using DFS Algorithm.
We build up a tree structure where the codons and the frequency of the codons are stored on each node. Then we use the depth-first search algorithm to traverse down from the root node successively, and match condon-frequence with the letter- frequency to obtain the correspondence between letters and codons.

The tree structure is shown in the figure 1.


Figure 1. Tree Structute.



3. Get the optimal solution by using optional algorithm.

In step 2, we get the correspondence between letters and codons. But some letters have multiple corresponding relationships. For example, in figure 1, the letters E and T correspond to codons GAU, GCU, GAA, E and T also correspond to codons GAU, GCU, AUG. What’s more, the letter T can also correspond to codons GAU, GCU, GCA. Therefore, we use the optimal algorithm to determine one of the multiple correspondence.

RESULTS

Print the correspondence between letters and codons

Output:

Draw letter-frequency histogram

Others

Visual Software

We developed a visual software. There are an input textbox, an output textbox, two radio buttons and a translate button in the software interface. We can choose radio buttons to select letters to codons or codons to letters. In addition to these, our software can also provide open files, copy files, cut files, save files, print files and other basic functions.
Software interface:



Letters to Codons:

Codons to letters:

Download

1.Coding 2.Visualization 3.Visualizaiton.exe