Team:HFUT CHINA/Human Practice.html

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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.

@@ Line 101: / Line 101: @@
 <div>
    <div>
-     <div>
+     <div >
        <span class="details">
        <h2 class="wrapper"><font class="font_1">Human Practice </font></h2>
@@ Line 108: / Line 108: @@
 			<p align="center" class="title_1"><img src="https://static.igem.org/mediawiki/2014/e/ee/Hfut-B7caedead8d0bebbaf4d2384e0bfe387.jpg" width="932" height="155"></p>
        </div>
-       <div>
+       <div style="width:80% ;padding-left:120px" >
-         <div align="left"></div>
+         <div align="left" ></div>
          <p>&nbsp;</p>
          <p>&nbsp;</p>
@@ Line 122: / Line 122: @@
          <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>
-         <table border="1" cellspacing="0" cellpadding="0" style=" margin-right: auto; margin-left: auto;background-color:#eee">
+         <table border="1" cellspacing="0" cellpadding="0" style=" margin-right: auto; margin-left: auto;background-color:#eee ;font-size:18px;width:100%" >
            <tr>
              <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">
-               <div align="justify">Type information extracted from database </div>
+               <div align="justify">Type information extracted<br> from database </div>
              </div></td>
-             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">Type information listed by Registry</p></td>
+             <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>
+           <td width="3" valign="top" class="style">&nbsp;</td>
+            <td width="323" valign="top" class="style">&nbsp;</td>
+            <td width="275" valign="top" class="style">&nbsp;</td>
+            <td width="288" valign="top" class="style">&nbsp;</td>
+</tr>
            <tr>
              <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="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>
+             <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>
            </tr>
@@ Line 140: / Line 146: @@
              <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="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>
+             <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>
            </tr>
@@ Line 146: / Line 152: @@
              <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="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>
+             <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>
            </tr>
@@ Line 152: / Line 158: @@
              <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="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>
+             <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>
            </tr>
@@ Line 158: / Line 164: @@
              <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="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>
+             <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>
            </tr>
@@ Line 164: / Line 170: @@
              <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="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>
+             <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>
            </tr>
@@ Line 170: / Line 176: @@
              <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="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>
+             <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>
            </tr>
@@ Line 182: / Line 188: @@
              <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="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>
+             <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>
            </tr>
@@ Line 206: / Line 212: @@
              <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="275" valign="top" class="style"><p align="justify" class="STYLE6"><a href="http://parts.igem.org/Promoters" title="Promoters">Promoters</a> </p></td>
+             <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>
            </tr>
@@ Line 212: / Line 218: @@
              <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="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>
+             <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>
            </tr>
@@ Line 224: / Line 230: @@
              <td width="3" valign="top" class="style">&nbsp;</td>
              <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Conjugation</p></td>
-             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">Protease site</p></td>
+             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6"></p></td>
              <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">Protease site</p></td>
            </tr>
@@ Line 230: / Line 236: @@
              <td width="3" valign="top" class="style">&nbsp;</td>
              <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Intermediate</p></td>
-             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">Protein stability element</p></td>
+             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6"></p></td>
              <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">Protein stability element</p></td>
            </tr>
@@ Line 236: / Line 242: @@
              <td width="3" valign="top" class="style">&nbsp;</td>
              <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">RNA</p></td>
-             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">Origin of replication</p></td>
+             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6"></p></td>
              <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">Origin of replication</p></td>
            </tr>
@@ Line 242: / Line 248: @@
              <td width="3" valign="top" class="style">&nbsp;</td>
              <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Temporary</p></td>
-             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">Assembly scar</p></td>
+             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6"></p></td>
              <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">Assembly scar</p></td>
            </tr>
@@ Line 248: / Line 254: @@
              <td width="3" valign="top" class="style">&nbsp;</td>
              <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Signalling</p></td>
-             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">Signature</p></td>
+             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6"></p></td>
              <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">Signature</p></td>
            </tr>
@@ Line 254: / Line 260: @@
              <td width="3" valign="top" class="style">&nbsp;</td>
              <td width="323" valign="top" class="style"><p align="justify" class="STYLE6">Project</p></td>
-             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6">User defined</p></td>
+             <td width="275" valign="top" class="style"><p align="justify" class="STYLE6"></p></td>
              <td width="288" valign="top" class="style"><p align="justify" class="STYLE6">User defined</p></td>
            </tr>
@@ Line 268: / Line 274: @@
              <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>
+           <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>
+            <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>
+</tr>
+          <tr>
+           <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>
          </table>