Team:HFUT CHINA/Human Practice.html

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Revision as of 01:10, 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

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 134: / Line 134: @@
              <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 140: @@
              <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 146: @@
              <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 152: @@
              <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 158: @@
              <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 164: @@
              <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 170: @@
              <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 182: @@
              <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 206: @@
              <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 212: @@
              <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>