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	Protease site
	Intermediate	Protein stability element	Protein stability element
	RNA	Origin of replication	Origin of replication
	Temporary	Assembly scar	Assembly scar
	Signalling	Signature	Signature
	Project	User defined	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.