Team:HFUT CHINA/Human Practice.html

From 2014.igem.org

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       <span class="details">
       <span class="details">
       <h2 class="wrapper"><font class="font_1">Human Practice </font></h2>
       <h2 class="wrapper"><font class="font_1">Human Practice </font></h2>
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<p align="center" class="title_1"><img src="https://static.igem.org/mediawiki/2014/e/ee/Hfut-B7caedead8d0bebbaf4d2384e0bfe387.jpg" width="932" height="155"></p>
<p align="center" class="title_1"><img src="https://static.igem.org/mediawiki/2014/e/ee/Hfut-B7caedead8d0bebbaf4d2384e0bfe387.jpg" width="932" height="155"></p>
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         <div align="left" ></div>
         <p>&nbsp;</p>
         <p>&nbsp;</p>
         <p>&nbsp;</p>
         <p>&nbsp;</p>
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         <p align="justify" class="STYLE2">Table 1 Comparison between type information extracted from database and type  information listed by Registry and SBOLv</p>
         <p align="justify" class="STYLE2">Table 1 Comparison between type information extracted from database and type  information listed by Registry and SBOLv</p>
         <p align="justify">&nbsp;</p>
         <p align="justify">&nbsp;</p>
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         <table border="1" cellspacing="0" cellpadding="0" style=" margin-right: auto; margin-left: auto;background-color:#eee ;font-size:20px" >
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         <table border="1" cellspacing="0" cellpadding="0" style=" margin-right: auto; margin-left: auto;background-color:#eee ;font-size:18px;width:100%" >
           <tr>
           <tr>
             <td width="1" valign="top" class="style"><div align="center" class="STYLE6"></div></td>
             <td width="1" valign="top" class="style"><div align="center" class="STYLE6"></div></td>
             <td width="323" valign="top" class="style"><div align="center" class="STYLE6">
             <td width="323" valign="top" class="style"><div align="center" class="STYLE6">
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               <div align="justify">Type information extracted from database </div>
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               <div align="justify">Type information extracted<br> from database </div>
             </div></td>
             </div></td>
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             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">Type information listed by Registry</p></td>
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             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">Type information listed <br>by Registry</p></td>
-
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">Type information listed in SBOLv</p></td>
+
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">Type information listed <br>in SBOLv</p></td>
           </tr>
           </tr>
 +
          <tr>
 +
          <td width="3" valign="top" class="style">&nbsp;</td>
 +
            <td width="323" valign="top" class="style">&nbsp;</td>
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            <td width="275" valign="top" class="style">&nbsp;</td>
 +
            <td width="288" valign="top" class="style">&nbsp;</td>
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</tr>
           <tr>
           <tr>
             <td width="3" valign="top" class="style"><p align="center" class="STYLE6">&nbsp;</p></td>
             <td width="3" valign="top" class="style"><p align="center" class="STYLE6">&nbsp;</p></td>
             <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Coding</p></td>
             <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Coding</p></td>
-
             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6"><a href="http://parts.igem.org/Protein_coding_sequences" title="Protein coding sequences">Protein coding sequences</a> </p></td>
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             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">Protein coding sequences</p></td>
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">cds</p></td>
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">cds</p></td>
           </tr>
           </tr>
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             <td width="3" valign="top" class="style">&nbsp;</td>
             <td width="3" valign="top" class="style">&nbsp;</td>
             <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Protein_Domain</p></td>
             <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Protein_Domain</p></td>
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             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6"><a href="http://parts.igem.org/Protein_domains" title="Protein domains">Protein domains</a> </p></td>
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             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">Protein domains</p></td>
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">Primer binding site</p></td>
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">Primer binding site</p></td>
           </tr>
           </tr>
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             <td width="3" valign="top" class="style">&nbsp;</td>
             <td width="3" valign="top" class="style">&nbsp;</td>
             <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Generator</p></td>
             <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Generator</p></td>
-
             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6"><a href="http://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=Generator">Protein generators</a> </p></td>
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             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">Protein generators</p></td>
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">Restriction site</p></td>
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">Restriction site</p></td>
           </tr>
           </tr>
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             <td width="3" valign="top" class="style">&nbsp;</td>
             <td width="3" valign="top" class="style">&nbsp;</td>
             <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Reporter</p></td>
             <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Reporter</p></td>
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             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6"><a href="http://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=reporter">Reporters</a> </p></td>
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             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">Reporters</p></td>
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">Blunt restriction site</p></td>
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">Blunt restriction site</p></td>
           </tr>
           </tr>
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             <td width="3" valign="top" class="style">&nbsp;</td>
             <td width="3" valign="top" class="style">&nbsp;</td>
             <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Measurement</p></td>
             <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Measurement</p></td>
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             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6"><a href="http://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=Measurement">Measurement    devices</a> </p></td>
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             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">Measurement    devices</p></td>
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">5’ sticky restriction site</p></td>
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">5’ sticky restriction site</p></td>
           </tr>
           </tr>
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             <td width="3" valign="top" class="style">&nbsp;</td>
             <td width="3" valign="top" class="style">&nbsp;</td>
             <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Translational_Unit</p></td>
             <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Translational_Unit</p></td>
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             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6"><a href="http://parts.igem.org/Translational_units" title="Translational units">Translational units</a> </p></td>
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             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">Translational units</p></td>
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">Operator</p></td>
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">Operator</p></td>
           </tr>
           </tr>
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             <td width="3" valign="top" class="style">&nbsp;</td>
             <td width="3" valign="top" class="style">&nbsp;</td>
             <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Composite</p></td>
             <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Composite</p></td>
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             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6"><a href="http://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=Composite">Composite parts</a> </p></td>
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             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">Composite parts</p></td>
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">3’ sticky restriction site</p></td>
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">3’ sticky restriction site</p></td>
           </tr>
           </tr>
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             <td width="3" valign="top" class="style">&nbsp;</td>
             <td width="3" valign="top" class="style">&nbsp;</td>
             <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Inverter</p></td>
             <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Inverter</p></td>
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             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6"><a href="http://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=inverter">Inverters</a> </p></td>
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             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">Inverters</p></td>
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">insulator</p></td>
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">insulator</p></td>
           </tr>
           </tr>
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             <td width="3" valign="top" class="style">&nbsp;</td>
             <td width="3" valign="top" class="style">&nbsp;</td>
             <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Regulatory</p></td>
             <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Regulatory</p></td>
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             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6"><a href="http://parts.igem.org/Promoters" title="Promoters">Promoters</a> </p></td>
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             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">Promoters</p></td>
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">Promoter</p></td>
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">Promoter</p></td>
           </tr>
           </tr>
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             <td width="3" valign="top" class="style">&nbsp;</td>
             <td width="3" valign="top" class="style">&nbsp;</td>
             <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Tag</p></td>
             <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Tag</p></td>
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             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6"><a href="http://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=Signalling">Receivers and    senders</a> </p></td>
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             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">Receivers and    senders</p></td>
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">3’ overhang</p></td>
             <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">3’ overhang</p></td>
           </tr>
           </tr>
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             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">&nbsp;</p></td>
             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">&nbsp;</p></td>
             <td width="288" valign="top" class="style">&nbsp;</td>
             <td width="288" valign="top" class="style">&nbsp;</td>
 +
</tr>
 +
          <tr>
 +
          <td width="3" valign="top" class="style">&nbsp;</td>
 +
            <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Cell</p></td>
 +
            <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">&nbsp;</p></td>
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            <td width="288" valign="top" class="style">&nbsp;</td>
 +
</tr>
 +
          <tr>
 +
          <td width="3" valign="top" class="style">&nbsp;</td>
 +
            <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Plasmid_Backbone</p></td>
 +
            <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">&nbsp;</p></td>
 +
            <td width="288" valign="top" class="style">&nbsp;</td>
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</tr>
 +
          <tr>
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          <td width="3" valign="top" class="style">&nbsp;</td>
 +
            <td width="323" valign="top" class="style"><p align="justify" class="STYLE6"> Primer</p></td>
 +
            <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">&nbsp;</p></td>
 +
            <td width="288" valign="top" class="style">&nbsp;</td>
 +
 +
           </tr>
           </tr>
         </table>
         </table>

Latest revision as of 02:09, 18 October 2014

HFUT_CHINA

Human Practice

 

 

Human practice:

 

Database

In order to support our software, we collected about 3600 device chains for analysis. All these devices’ information are stored in our database. Besides, we analyze the associate relationship between biobricks in these chains, and these associate relationship information are also stored in our database. We shared this database with developers who want to use these information for analyzing. The detailed API for database could be found

here

 

Symbols for Biobricks

When implementing our software, we want to visualize the designed device. Since each biobrick in Registry have a type, the biobricks with the same type should be visualized with the same symbols. Hence, we extracted the type information from Registry database, and compared them with the type information listed by Registry and SBOLv. Table 1 shows the results.

 

Table 1 Comparison between type information extracted from database and type information listed by Registry and SBOLv

 

Type information extracted
from database

Type information listed
by Registry

Type information listed
in SBOLv

       

 

Coding

Protein coding sequences

cds

 

Protein_Domain

Protein domains

Primer binding site

 

Generator

Protein generators

Restriction site

 

Reporter

Reporters

Blunt restriction site

 

Measurement

Measurement devices

5’ sticky restriction site

 

Translational_Unit

Translational units

Operator

 

Composite

Composite parts

3’ sticky restriction site

 

Terminator

Terminator

Terminator

 

Inverter

Inverters

insulator

 

RBS

RBS

Ribosome entry site

 

Plasmid

Plasmids

5’ overhang

 

DNA

DNA

Ribonuclease site

 

Regulatory

Promoters

Promoter

 

Tag

Receivers and senders

3’ overhang

 

Device

Plasmid backbones

Rna stability element

 

Conjugation

Protease site

 

Intermediate

Protein stability element

 

RNA

Origin of replication

 

Temporary

Assembly scar

 

Signalling

Signature

 

Project

User defined

 

T7

 

 

Other

 

 
 

Cell

 

 
 

Plasmid_Backbone

 

 
 

Primer

 

 

 

We choose SBOLv symbols to represent the biobricks. As some types in Registry are actually device, such as Reporter, Generator, DNA, etc, these types are represented with the same symbol.