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Revision as of 01:16, 18 October 2014
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
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.
