Systems and methods for facilitating modular and parallelized manufacturing at a biological foundry

A computer system for implementing one or more compiled workflows, the computer system comprising one or more processors, a memory storing one or more programs for execution by the one or more processors, a controller, a communications interface in electrical communication with at least a power supply and a plurality of peripheral devices comprising an articulated handling robot, wherein the articulated handling robot is configured to advance the one or more compiled workflows from one or more instruments in a plurality of instruments, wherein each respective instrument in the plurality of instruments is associated with a corresponding biological foundry operation in a plurality of biological foundry operations;

• the one or more programs singularly or collectively using the one or more processors to execute a method comprising:
• (A) obtaining, in electronic form, from a remote device, a representation of an uncompiled workflow that is configured to produce a first plurality of organic engineering targets, wherein the uncompiled workflow is associated with a predetermined set of a plurality of workflow operations, each workflow operation in the plurality of workflow operations being an operation in the plurality of biological foundry operations and defined by an administrator of the remote device, and wherein the plurality of workflow operations is temporally ordered in accordance with a decision tree defined by the administrator and a plurality of heuristic constraints;
• (B) translating, via the controller, using a first set of nodes in a plurality of nodes of the decision tree, for each respective organic engineering target in the first plurality of organic engineering targets, the representation of the uncompiled workflow into a first corresponding instance of a compiled workflow for the respective organic engineering target in accordance with the plurality of heuristic constraints associated with the representation of the uncompiled workflow, wherein the first corresponding instance of the compiled workflow comprises:
• (i) for each respective instrument in a subset of instruments of the plurality of instruments:
• (a) a corresponding position in the temporal order of the plurality of workflow operations based on the corresponding biological foundry operation associated with the respective instrument, and
• (b) one or more corresponding execution instructions comprising a corresponding first traverse instruction commanding the articulated handling robot to move to at least one corresponding spatial coordinate associated with the respective instrument;
• (C) determining, via the controller, if the translating (B) satisfies each threshold translation criterion in a plurality of threshold translation criteria associated with the translation of the uncompiled workflow, wherein a first threshold translation criterion comprises a performance score based on a comparison of the representation of the uncompiled workflow and the compiled workflow and defined at least in part, by the decision tree;
• (D) executing, in accordance with a determination the translating (B) satisfies each threshold translation criterion in the plurality of threshold translation criteria of the determining (C), the first corresponding instance of the compiled workflow, thereby completing a first portion of the manufacture of the plurality of organic engineering targets;
• (E) determining, via the controller, if a status of the executing (D) satisfies each threshold execution criterion in a plurality of threshold execution criterion associated with the translation of the uncompiled workflow, wherein a first threshold execution criterion is associated with a disruption associated with a condition associated with the computer system defined by the decision tree;
• (F) translating, via the controller, using a second set of nodes, different from the first plurality of nodes, in the plurality of nodes of the decision tree, for each respective organic engineering target in the first plurality of organic engineering targets, the representation of the uncompiled workflow into a second corresponding instance of the compiled workflow for the respective organic engineering target in accordance with the plurality of heuristic constraints associated with the representation of the uncompiled workflow, wherein the second corresponding instance of the compiled workflow comprises:
• (i) for a first instrument in the subset of instruments of the plurality of instruments:
• (a) a second position other than a first position in the temporal order of the plurality of workflow operation of the first instrument in the first corresponding instance of the compiled workflow, and
• (b) one or more execution instructions comprising a second traverse instruction commanding the articulated handling robot to move to at least one spatial coordinate associated with the first instrument when executing the second position in the temporal order of the plurality of workflow operation;
• (G) determining, via the controller, if the translating (F) satisfies each threshold translation criterion in the plurality of threshold translation criteria;
• and
• (H) executing, in accordance with a determination the translating (F) satisfies each threshold translation criterion in the plurality of threshold translation criteria of the determining (G), the second corresponding instance of the compiled workflow, thereby completing the second portion of the manufacture of the plurality of organic engineering targets.

A non-transitory computer readable storage medium storing one or more programs, the one or more programs comprising instructions, which when executed by a computer system at a biological foundry, the biological foundry comprising one or more processors, a memory storing one or more programs for execution by the one or more processors, a controller, a communications interface in electrical communication with at least a power supply and a plurality of peripheral devices comprising an articulated handling robot, wherein the articulated handling robot is configured to advance the one or more compiled workflows from one or more instruments in a plurality of instruments, wherein each respective instrument in the plurality of instruments is associated with a corresponding biological foundry operation in a plurality of biological foundry operations, cause the computer system to perform a method comprising:

• (A) obtaining, in electronic form, from a remote device, a representation of an uncompiled workflow that is configured to produce a first plurality of organic engineering targets at a plurality of biological foundries, wherein the uncompiled workflow is associated with a predetermined set of a plurality of workflow operations, each workflow operation in the plurality of workflow operations being an operation in the plurality of biological foundry operations and defined by an administrator of the remote device, and wherein the plurality of workflow operations is temporally ordered in accordance with a decision tree defined by the administrator and a plurality of heuristic constraints;
• (B) translating, via the controller, using a first set of nodes in a plurality of nodes of the decision tree, for each respective organic engineering target in the first plurality of organic engineering targets, the representation of the uncompiled workflow into a first corresponding instance of a compiled workflow for the respective organic engineering target in accordance with the plurality of heuristic constraints associated with the representation of the uncompiled workflow, wherein the first corresponding instance of the compiled workflow comprises:
• (i) for each respective instrument in a subset of instruments of the plurality of instruments:
• (a) a corresponding position in the temporal order of the plurality of workflow operations based on the corresponding biological foundry operation associated with the respective instrument, and
• (b) one or more corresponding execution instructions comprising a corresponding first traverse instruction commanding the articulated handling robot to move to at least one corresponding spatial coordinate associated with the respective instrument;
• (C) determining, via the controller, if the translating (B) satisfies each threshold translation criterion in a plurality of threshold translation criteria associated with the translation of the uncompiled workflow, wherein a first threshold translation criterion comprises a performance score based on a comparison of the representation of the uncompiled workflow and the compiled workflow and defined at least in part, by the decision tree;
• (D) executing, in accordance with a determination the translating (B) satisfies each threshold translation criterion in the plurality of threshold translation criteria of the determining (C), the first corresponding instance of the compiled workflow, thereby completing a first portion of the manufacture of the plurality of organic engineering targets;
• (E) determining, via the controller, if a status of the executing (D) satisfies each threshold execution criterion in a plurality of threshold execution criterion associated with the translation of the uncompiled workflow, wherein a first threshold execution criterion is associated with a disruption associated with a condition at the biological foundry defined by the decision tree;
• (F) translating, via the controller, using a second set of nodes, different from the first plurality of nodes, in the plurality of nodes of the decision tree, for each respective organic engineering target in the first plurality of organic engineering targets, the representation of the uncompiled workflow into a second corresponding instance of the compiled workflow for the respective organic engineering target in accordance with the plurality of heuristic constraints associated with the representation of the uncompiled workflow, wherein the second corresponding instance of the compiled workflow comprises:
• (i) for a first instrument in the subset of instruments of the plurality of instruments:
• (a) a second position other than a first position in the temporal order of the plurality of workflow operation of the first instrument in the first corresponding instance of the compiled workflow, and
• (b) one or more execution instructions comprising a second traverse instruction commanding the articulated handling robot to move to at least one spatial coordinate associated with the first instrument when executing the second position in the temporal order of the plurality of workflow operation;
• (G) determining, via the controller, if the translating (F) satisfies each threshold translation criterion in the plurality of threshold translation criteria;
• and
• (H) executing, in accordance with a determination the translating (F) satisfies each threshold translation criterion in the plurality of threshold translation criteria of the determining (G), the second corresponding instance of the compiled workflow, thereby completing the second portion of the manufacture of the plurality of organic engineering targets.