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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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Overview of the SynBioLGDB database.
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f1: Overview of the SynBioLGDB database.

Mentions: Because genetic logic gates are the basic building biobricks of electronic circuits we developed a synthetic biology database of experimentally validated logic gates (SynBioLGDB, http://bioinformatics.ac.cn/synbiolgdb/) to facilitate related research. This database is aimed at gathering a comprehensive collection of experimentally validated logic gates by manually curating the literature (Figure 1). The current version of SynBioLGDB documents more than 180 logic gates across three species (Human, Escherichia coli and Bacillus clausii). SynBioLGDB therefore provides a global view of genetic logic gates in synthetic biology. Researchers can follow these genetic logic gates to explore how the input and output of genes, proteins and promoters are organized. The whole data set can be easily queried and downloaded from the website. In addition, SynBioLGDB allows researchers to submit new 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)

Overview of the SynBioLGDB database.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Overview of the SynBioLGDB database.
Mentions: Because genetic logic gates are the basic building biobricks of electronic circuits we developed a synthetic biology database of experimentally validated logic gates (SynBioLGDB, http://bioinformatics.ac.cn/synbiolgdb/) to facilitate related research. This database is aimed at gathering a comprehensive collection of experimentally validated logic gates by manually curating the literature (Figure 1). The current version of SynBioLGDB documents more than 180 logic gates across three species (Human, Escherichia coli and Bacillus clausii). SynBioLGDB therefore provides a global view of genetic logic gates in synthetic biology. Researchers can follow these genetic logic gates to explore how the input and output of genes, proteins and promoters are organized. The whole data set can be easily queried and downloaded from the website. In addition, SynBioLGDB allows researchers to submit new 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