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SynBioLGDB: a resource for experimentally validated logic gates in synthetic biology.

Wang L, Qian K, Huang Y, Jin N, Lai H, Zhang T, Li C, Zhang C, Bi X, Wu D, Wang C, Wu H, Tan P, Lu J, Chen L, Li K, Li X, Wang D - Sci Rep (2015)

Bottom Line: Increasing evidence has also revealed that diverse genetic logic gates capable of generating a Boolean function play critically important roles in synthetic biology.Basic genetic logic gates have been designed to combine biological science with digital logic.SynBioLGDB will enable more comprehensive understanding of the connection of genetic logic gates to execute complex cellular functions in living cells.

View Article: PubMed Central - PubMed

Affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.

ABSTRACT
Synthetic biologists have developed DNA/molecular modules that perform genetic logic operations in living cells to track key moments in a cell's life or change the fate of a cell. Increasing evidence has also revealed that diverse genetic logic gates capable of generating a Boolean function play critically important roles in synthetic biology. Basic genetic logic gates have been designed to combine biological science with digital logic. SynBioLGDB (http://bioinformatics.ac.cn/synbiolgdb/) aims to provide the synthetic biology community with a useful resource for efficient browsing and visualization of genetic logic gates. The current version of SynBioLGDB documents more than 189 genetic logic gates with experimental evidence involving 80 AND gates and 16 NOR gates, etc. in three species (Human, Escherichia coli and Bacillus clausii). SynBioLGDB provides a user-friendly interface through which conveniently to query and browse detailed information about these genetic logic gates. SynBioLGDB will enable more comprehensive understanding of the connection of genetic logic gates to execute complex cellular functions in living cells.

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Pie chart of the logic gate categories in the SynBioLGDB database.
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f2: Pie chart of the logic gate categories in the SynBioLGDB database.

Mentions: In the current version, SynBioLGDB documents 80 AND gates, 8 Buffer gates, 7 Combinatorial gates, 10 NAND gates, 16 NOR gates, 28 NOT gates, 17 OR gates, 7 XOR gates and 16 other gates (Figure 2) across three species (Human, Escherichia coli and Bacillus clausii)16. Each entry contains detailed information on a logic gate in the ‘Detail' page, including gate category, input gene/protein/promoter symbols, output gene/protein/promoter symbols, species, validated method, PubMed Identifier (PMID) and detailed description. SynBioLGDB also provides three options on the ‘Help' page, with instructions for using the database. These include ‘Tutorial' (procedure and illustrations of the database), ‘Statistics' (detailed statistical tables) and ‘Error Report'. In the ‘Download & API' page, users can download all logic gate data in Microsoft Excel and TXT format by selecting ‘SynBioLGDB all data', or access the application programming interface (API) using scripts. In the ‘Submit' page, SynBioLGDB invites users to submit novel logic gates.


SynBioLGDB: a resource for experimentally validated logic gates in synthetic biology.

Wang L, Qian K, Huang Y, Jin N, Lai H, Zhang T, Li C, Zhang C, Bi X, Wu D, Wang C, Wu H, Tan P, Lu J, Chen L, Li K, Li X, Wang D - Sci Rep (2015)

Pie chart of the logic gate categories in the SynBioLGDB database.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4308699&req=5

f2: Pie chart of the logic gate categories in the SynBioLGDB database.
Mentions: In the current version, SynBioLGDB documents 80 AND gates, 8 Buffer gates, 7 Combinatorial gates, 10 NAND gates, 16 NOR gates, 28 NOT gates, 17 OR gates, 7 XOR gates and 16 other gates (Figure 2) across three species (Human, Escherichia coli and Bacillus clausii)16. Each entry contains detailed information on a logic gate in the ‘Detail' page, including gate category, input gene/protein/promoter symbols, output gene/protein/promoter symbols, species, validated method, PubMed Identifier (PMID) and detailed description. SynBioLGDB also provides three options on the ‘Help' page, with instructions for using the database. These include ‘Tutorial' (procedure and illustrations of the database), ‘Statistics' (detailed statistical tables) and ‘Error Report'. In the ‘Download & API' page, users can download all logic gate data in Microsoft Excel and TXT format by selecting ‘SynBioLGDB all data', or access the application programming interface (API) using scripts. In the ‘Submit' page, SynBioLGDB invites users to submit novel logic gates.

Bottom Line: Increasing evidence has also revealed that diverse genetic logic gates capable of generating a Boolean function play critically important roles in synthetic biology.Basic genetic logic gates have been designed to combine biological science with digital logic.SynBioLGDB will enable more comprehensive understanding of the connection of genetic logic gates to execute complex cellular functions in living cells.

View Article: PubMed Central - PubMed

Affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.

ABSTRACT
Synthetic biologists have developed DNA/molecular modules that perform genetic logic operations in living cells to track key moments in a cell's life or change the fate of a cell. Increasing evidence has also revealed that diverse genetic logic gates capable of generating a Boolean function play critically important roles in synthetic biology. Basic genetic logic gates have been designed to combine biological science with digital logic. SynBioLGDB (http://bioinformatics.ac.cn/synbiolgdb/) aims to provide the synthetic biology community with a useful resource for efficient browsing and visualization of genetic logic gates. The current version of SynBioLGDB documents more than 189 genetic logic gates with experimental evidence involving 80 AND gates and 16 NOR gates, etc. in three species (Human, Escherichia coli and Bacillus clausii). SynBioLGDB provides a user-friendly interface through which conveniently to query and browse detailed information about these genetic logic gates. SynBioLGDB will enable more comprehensive understanding of the connection of genetic logic gates to execute complex cellular functions in living cells.

Show MeSH
Related in: MedlinePlus