Compiler for Genetic Device Design Using Logical Constraints
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Solution Overview
Problem
The design and construction of genetic devices for microorganisms is a time-consuming and costly process, often relying on trial-and-error methods, and existing computer languages require exact specification of DNA sequences, limiting the flexibility in designing genetic devices.
Innovation Solution
A computer system that receives input specifying part designs with logical variables and constraints, using a database of genetic parts and reactions to generate candidate devices, which can be simulated and implemented in biological systems, allowing for the creation of genetic devices with specified properties and behaviors.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If trial-and-error methods are used to design and construct genetic devices, then flexibility in exploring different designs is improved, but time consumption and cost increase
Solution Approach 1:
The system performs preliminary computational analysis and simulation of genetic device designs before actual construction. The computer system evaluates multiple design candidates in silico, predicting their behavior and performance, so that only the most promising designs are constructed in the lab, avoiding time-consuming trial-and-error with unsuccessful designs
Solution Approach 2:
The system creates virtual models and simulations of genetic devices as digital copies before building physical versions. These computational models allow researchers to test and refine designs in a virtual environment, reducing the need for repeated physical construction and testing of unsuccessful designs
2Manufacturing precision
If existing computer languages require exact specification of DNA sequences, then precision in design specification is improved, but flexibility in designing genetic devices decreases
Solution Approach 1:
The system changes the parameters of design specification from requiring exact DNA sequences to accepting functional requirements and desired behaviors. Instead of specifying precise genetic sequences, users can define what the genetic device should accomplish, and the system automatically generates appropriate sequences that meet these functional specifications
Solution Approach 2:
The system inverts the traditional design approach by working backwards from desired functional outcomes to determine the appropriate DNA sequences. Rather than starting with specific sequences and predicting their function, the system takes the functional requirements first and computationally derives the genetic implementations that will achieve those functions
3Reliability
If multiple design candidates are generated and simulated, then the quality of selected genetic devices is improved, but computational resources and time increase
Solution Approach 1:
The system generates a limited number of high-quality design candidates rather than exhaustively evaluating all possible designs. By using intelligent algorithms to prioritize promising designs and stop simulation when sufficient candidates are found, the system achieves reliable device selection without excessive computational resource consumption
Data Source
AI summary
Creating genetic devices for use in micro-organisms or other biological systems is described. In an embodiment a computer system receives at a program editor, input specifying a plurality of part designs, at least some of which comprise part properties expressed as logical variables; and the input also specifies constraints on the logical variables. For example, the input is a computer program which specifies constraints on the logical variables which, for example, relate to properties of the DNA sequences such as reactions and biological behaviors. In an example, a compiler resolves the constraints using a database of genetic parts in order to generate candidate parts for the proposed genetic device. In examples the sequences of genetic parts are translated into reactions and simulated using an automated simulator and/or implemented in a living cell or other biological system. In embodiments the compiler also uses a database of reactions.