Software-based systems and methods for designing and implementing high-order gate layouts for synthetic logic circuits

A method for generating an application-specific, modular circuit vector to implement a set of logic functions comprising:

• receiving user input comprising data indicative of:
• a crop variety of interest, one or more desired traits, one or more undesired traits, and one or more genes of interest;
• accessing a library of gene information pertaining to the crop variety of interest, to obtain gene activation information relating to the one or more desired traits, one or more undesired traits, and one or more genes of interest;
• using the gene activation information, generating a circuit layout comprising a plurality of logic gates wherein an input channel to the circuit layout corresponds to an input that affects the one or more genes of interest to affect the one or more desired traits and the one or more undesired traits;
• compiling a modular vector to encode the logic gates in the circuit layout for the crop variety of interest by:
• identifying a stored vector construct, from a database of vector constructs, for each class of logic gate used in the circuit layout;
• customizing the vector constructs to encode at least one logic gate input for each vector construct, the logic gate input associated with either:
• inputs identified as part of the gene activation information, or logic gate outputs of other vector constructs within the circuit layout;
• customizing at least one of the vector constructs to encode a logic gate output associated with the one or more genes of interest;
• combining the customized vector constructs to form the modular vector expressing the designed circuit layout;
• and
• outputting a file to the user comprising sequence information of a DNA vector corresponding to the modular vector.