Creating genetic devices

A method of creating a genetic device, the method comprising:

• establishing a connection to a database of genetic parts, an entry of the database including an identifier of a deoxyribonucleic acid (DNA) sequence and at least one part property that includes a binding rate specified for gene expression of the DNA sequence;
• receiving, by a program editor, input specifying a plurality of genetic parts, the plurality of genetic parts including at least one unspecified genetic part that is represented by use of a logical variable together with one or more properties without exact specification of a DNA sequence to be used, wherein the one or more properties are expressed in terms of logical variables that impose constraints on the unspecified genetic part, the constraints including a rate having a specified range;
• resolving, at a compiler, the constraints using specified semantics to provide at least one possible genetic device template comprising a list of part variables and substitutions on the part variables that, when applied to the genetic device template, results in a list of genetic parts which satisfies the constraints, wherein the specified semantics comprise:
• identifying a genetic part,
• identifying an empty device template and an empty part substitution,
• binding a module name to a function given one or more parameters,
• looking up the module name,
• invoking the function bound to the module name,
• producing a part sequence,
• producing a union of two part sequences,
• producing a sequential composition of the two part sequences,
• creating a compartment-specific part sequence,
• substituting a new variable for the logical variable, the new variable not occurring elsewhere in the sequence of genetic parts,
• creating a set of context-sensitive substitutions,
• ignoring compartment names in transport reactions,
• identifying substitutions that satisfy a numerical constraint, and
• combining context-sensitive substitutions arising from the numerical constraint;
• establishing a connection to a database of reactions each associated with one or more constraints;
• translating, at the compiler, the at least one possible genetic device template and the constraints provided by the input to at least one reaction from the database of reactions;
• receiving a selection of the at least one reaction for a simulation;
• conducting the simulation after the constraints have been satisfied, the simulation being based at least in part on an explicit host physiology;
• evaluating the at least one possible genetic device template based at least in part on results of the simulation;
• and
• manufacturing a genetic device selected based at least in part upon the results of the simulation.

A system comprising:

• an input arranged to connect to a genetic parts database of parts representing deoxyribonucleic acid (DNA) sequences, each part comprising a part type selected from a group comprising a promoter, a ribosome binding site, and a protein coding region;
• a unique identifier of a DNA sequence;
• at least one part property selected from a group comprising activation by a transcription factor, inhibition by a transcription factor, binding rate, unbinding rate, interaction with a protein, and rate of protein degradation;
• a program editor configured to receive a program input specifying a plurality of the parts, an ordering of the parts, and at least one constraint on at least one of the parts;
• a memory storing rules embodying denotational semantics of a language of the program input;
• a compiler arranged to resolve the at least one constraint, the at least one constraint consisting of biological behaviors, reactions of DNA sequences, or a combination thereof, using the at least one part property while accounting for interactions between DNA sequences of the parts received in the program input to provide a device template comprising at least one sequence of parts from the genetic parts database which satisfies the at least one constraint, the at least one constraint being specified without identification of sequences of the DNA sequences of the parts, wherein the resolving includes:
• identifying a genetic part,
• identifying an empty device template and an empty part substitution,
• binding a module name to a function given one or more parameters,
• looking up the module name,
• invoking the function bound to the module name,
• producing a part sequence, producing a union of two part sequences,
• producing a sequential composition of the two part sequences,
• creating a compartment-specific part sequence,
• substituting a new variable for the logical variable, the new variable not occurring elsewhere in the sequence of genetic parts,
• creating a set of context-sensitive substitutions,
• ignoring compartment names in transport reactions,
• identifying substitutions that satisfy a numerical constraint, or
• combining context-sensitive substitutions arising from the numerical constraint;
• an automated simulator configured to simulate a plurality of sequences of parts generated by the compiler;
• and
• a genetic device manufacturing system configured to create a sequence of parts of the plurality of sequences of parts in a living cell, the sequence of parts selected based at least in part on results of the automated simulator.