Methods and systems for designing machines including biologically-derived parts
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Abstract
A preferred embodiment of the present invention comprises computer-implemented methods for providing user assistance in biomachine design that, first, retrieve one or more digitally-represented candidate design items stored in a bioengineering knowledge base by translating requirements provided for a biomachine according to a bioengineering domain model into queries to the knowledge base for design items capable of implementing the biomachine according to the domain model; then second, construct one or more digitally-represented candidate biomachines from the candidate design items by arranging part information represented in the candidate design items according to a selected structure, and next evaluate the candidate biomachines according to bioengineering operability knowledge associated with the candidate design items, wherein operability knowledge associated with a design item specifies requirements for that item to inter-operate with other design items. The methods may backtrack. If at least one candidate biomachine has not been satisfactorily evaluated, the methods backtracking to one or more of these steps. The invention further encompasses variations of these methods, systems and program products performing these methods, data products including digital representations of design knowledge used by these methods, data products with digital representations of designed biomachines. Also encompassed are further steps of constructing or synthesizing biomachines along with the actual biomachines themselves.
41 Citations
109 Claims
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1-89. -89. (canceled)
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90. A computer-implemented method for providing user assistance in biomolecular biomachine design comprising:
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(a) providing a bioengineering knowledge base comprising part-type design items comprising biochemical, protein, genetic, cellular, or multi-cellular items including physical description information and behavior information;
(b) retrieving from said knowledge base one or more digitally-represented candidate biomolecular design items by translating requirements provided for a said biomolecular biomachine according to a bioengineering domain model into queries to the knowledge base for design items capable of implementing the biomachine according to the domain model, (c) constructing one or more digitally-represented candidate biomachines from the candidate design items by arranging part information represented in the candidate design items according to a selected structure, and (d) evaluating the candidate biomachines according to bioengineering operability knowledge associated with the candidate design items, wherein operability knowledge associated with a design item specifies requirements for that item to inter-operate with other design items. - View Dependent Claims (91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103)
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104. A computer-implemented method for providing user assistance in biomolecular biomachine design comprising:
- (a) translating requirements provided for a biomachine according to a bioengineering domain model into one or more digitally-represented candidate design items comprising biomolecular part information, the candidate design items represented being capable of implementing the biomachine requirements according to the domain model, and (b) constructing one or more candidate biomachines from the candidate design items by arranging the part information represented in the candidate design items according to a selected structure, whereby the candidate biomachines provide user biomachine-design assistance.
- View Dependent Claims (105, 106, 107, 108)
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109. A computer-readable medium having biomolecular biomachine design knowledge digitally encoded therein, the design knowledge comprising representations of:
- (a) biomolecular design items including structure information and part information, wherein a plurality of biomachine can be represented by combinations of part information according to structure information, and (b) bioengineering operability knowledge associated with the candidate design items, wherein operability knowledge associated with a design item specifies requirements for that item to inter-operate with other design items.
Specification