Device-agnostic system for planning and executing high-throughput genomic manufacturing operations

One or more non-transitory computer-readable media storing instructions for generating a build graph data structure to control production in a gene manufacturing system of at least one product of interest incorporating genetic modifications, wherein the instructions, when executed by one or more computing devices, cause at least one of the one or more computing devices to:

• access a description of a biological workflow, wherein the description includes representations of biological components;
• and
• assemble a build graph data structure based at least in part upon the workflow description,
• wherein, in the build graph data structure, each biological component is represented by a node that resides at a level of a plurality of levels,
• wherein one or more source nodes, at a given level of the plurality of levels, and a destination node, at a child level of the given level, constitute a reaction group of one or more reaction groups corresponding to the child level,
• wherein each reaction group represents a reaction between one or more biological components that are themselves represented by the one or more source nodes at the given level, to produce a biological component represented by the destination node of the reaction group at the child level,
• wherein one or more destination nodes at the child level act as one or more source nodes in a reaction group of one or more reaction groups at a grandchild level of the given level, and
• wherein at least one destination node at a final level of the plurality of levels represents the at least one product of interest, which incorporates genetic modifications caused by reactions among biological components at different levels, and
• wherein processing the build graph data structure results in production of the at least one product of interest.

One or more non-transitory computer-readable media storing instructions for processing factory orders to control production in a gene manufacturing system of one or more products of interest incorporating genetic modifications, wherein the instructions, when executed by one or more computing devices, cause at least one of the one or more computing devices to:

• access a plurality of factory orders, wherein each factory order indicates one or more genetic design techniques for building one or more products of interest;
• determine that two or more workflow phases for workflows for constructing different factory orders of the plurality of factory orders are common workflow phases that may be processed together based at least in part upon a commonality of reaction steps of the common workflow phases, wherein each workflow comprises a series of workflow phases, and each workflow phase comprises one or more reaction steps;
• and
• generate a build graph data structure based at least in part upon the common workflow phases, wherein processing the build graph data structure results in production of the one or more products of interest.

One or more non-transitory computer-readable media storing instructions for processing a build graph data structure to control production in a gene manufacturing system of a product of interest that incorporates genetic modifications, wherein the instructions, when executed by one or more computing devices, cause at least one of the one or more computing devices to:

• access a build graph data structure comprising a plurality of nodes, wherein
• each node represents a biological component and resides at a level of a plurality of levels,
• one or more source nodes, at given level of the plurality of levels, and a destination node, at a child level of the given level, constitute a reaction group of one or more reaction groups corresponding to the child level, and
• each reaction group represents a reaction between the one or more biological components that are themselves represented by the one or more source nodes at the given level to produce a biological component represented by the destination node of the reaction group at the child level;
• and
• traverse the build graph data structure at the plurality of levels to map the biological components corresponding to the nodes at the plurality of levels to physical laboratory equipment, wherein operation of the physical laboratory equipment leads to production of the product of interest.

One or more non-transitory computer-readable media storing instructions for implementation of biological protocols on a plurality of automated equipment to generate a product of interest that incorporates genetic modifications, wherein different ones of the automated equipment implement biological protocols pursuant to machine-specific instructions in respective, different machine-specific languages, wherein the instructions, when executed by one or more computing devices, cause at least one of the one or more computing devices to:

• issue object instructions based at least in part upon one or more factory orders, the object instructions for instructing the plurality of automated equipment to execute biological protocols;
• and
• translate object instructions into machine-specific instructions in a machine-specific language of a plurality of machine-specific languages,
• wherein each automated equipment is operable to execute machine-specific instructions in a respective machine-specific language to implement a biological protocol to generate a biological component along a path to generating the product of interest, and at least two automated equipment operate pursuant to different machine-specific languages.

One or more non-transitory computer-readable media storing instructions for designing quality testing of a plurality of biological components, wherein the instructions, when executed by one or more computing devices, cause at least one of the one or more computing devices to:

• perform, in silico, one or more assays on one or more target biological components, the in silico performance of each assay on one of the one or more biological components producing one or more assay reaction products resulting from an assay reaction involving the one of the one or more target biological components;
• classify two or more expected outcomes of each assay as being from the group of:
• at least one success mode or at least one failure mode, based at least in part upon empirical information concerning the assay;
• and
• store, in an assay data structure, for the one or more assay reaction products, reference information including:
• (a) attributes of the one or more assay reaction products, and (b) the classification of the two or more expected outcomes,
• wherein processing of the assay data structure results in:
• (a) performing one or more physical assays, corresponding to the one or more in silico assays, on the one or more target biological components using physical laboratory equipment to generate one or more physical assay reaction products for each physical assay, and (b) for each physical assay, comparing the one or more physical assay reaction products to corresponding reference information to classify the target biological component as corresponding to the at least one success mode or the at least one failure mode.

One or more non-transitory computer-readable media storing instructions for performing quality testing of a target biological component, wherein the instructions, when executed by one or more computing devices, cause at least one of the one or more computing devices to:

• obtain information concerning one or more physical assay reaction products resulting from a physical assay of a target biological component;
• and
• compare the one or more physical assay reaction products to corresponding reference information to classify the target biological component as corresponding to at least one success mode, to at least one failure mode, or to an indeterminate mode,
• wherein the reference information includes expected attributes of the one or more physical assay reaction products corresponding to success and failure modes.

One or more non-transitory computer-readable media storing instructions for generating a factory order to control production of biological sequences by a gene manufacturing system, wherein the instructions, when executed by one or more computing devices, cause at least one of the one or more computing devices to:

• receive an expression indicating a non-deterministic operation on a first sequence operand, wherein sequence operands represent biological sequence parts, the first sequence operand representing one or more biological sequence parts;
• execute instructions to evaluate the expression to a sequence specification, wherein the sequence specification comprises a data structure including (a) one or more first-level non-deterministic operations, including the first non-deterministic operation, to be performed on one or more first-level sequence operands including the first sequence operand, and (b) one or more second-level operations, the execution of which resolves one or more values of the one or more first-level sequence operands;
• and
• generate a factory order based upon execution, by a computing device, of one or more of the first-level operations and one or more of the second-level operations, the factory order for use by the gene manufacturing system to generate biological sequence parts, wherein the one or more first-level non-deterministic operations correspond to protocols for generating the biological sequence parts.