What is synthetic biology? In simple words Synthetic biology is nothing but putting engineering into biology. An engineered genetic toggle switch developed by Tim Gardner and Jim Collins is a good example of how engineering principles are driving the boat of synthetic biology. Researchers are now trying to adapt concepts developed in area of programming language development & software engineering for synthetic biology applications. A latest paper in PLoS Computational Biology shows how methods used by computer scientists to develop programming languages can be applied to DNA sequences. They report an attribute grammar based formalism to model the structure-function relationships in synthetic DNA sequences. An attribute grammar is constructed as an extension of a context-free grammar and in computer science it is commonly used to translate the text of a program source code or the syntax tree directly into the computational operations or machine level instructions. Further
The translation of a gene network model from a genetic sequence is very similar to the compilation of the source code of a computer program into an object code that can be executed by a microprocessor (Figure 1). The first step consists in breaking down the DNA sequence into a series of genetic parts by a program called the lexer or scanner. Since the sequence of a part may be contained in the sequence of another part, the lexer is capable of backtracking to generate all the possible interpretations of the input DNA sequences as a series of parts. All possible combinations of parts generated by the lexer are sent to a second program called the parser to analyze if they are structurally consistent with the language syntax. The structure of a valid series of parts is represented by a parse tree (Figure 2). The semantic evaluation takes advantage of the parse tree to translate the DNA sequence into a different representation such as a chemical reaction network. The translation process requires attributes and semantic actions. Attributes are properties of individual genetic parts or combinations of parts. Semantic actions are associated with the grammar production rules. They specify how attributes are computed. Specifically, the translation process relies on the semantic actions associated with parse tree nodes to synthesize the attributes of the construct from the attributes of its child nodes, or to inherit the attributes from its parental node.
Figure. 1
Figure 2.Proposed formalism can be quite useful to understand how a set of genetic components relates to a function with potential to assemble a new biological systems of desired functionality or phenotype using BioBricks standard biological parts. It will be implemented into GenoCAD, a web-based tool used for genetic engineering of cells.
This blog provide great description about how engineering principles are driving the boat of synthetic biology.. Diagrammatic representation focus on The translation of a gene network model from a genetic sequence is really interesting and easily helps to understand the process.Thanx for sharing such informative and useful post
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