Systems and methods for facilitating modular and parallelized manufacturing at a biological foundry
Systems and methods for implementing one or more compiled workflows at a biological foundry are provided. A representation of an uncompiled workflow to produce engineering targets is obtained. The representation is translated into a first corresponding instance of a compiled workflow. If the translation satisfaction of various threshold translation criteria is determined, and the first corresponding instance of the compiled workflow is executed to complete a first portion of manufacture of the engineering targets. If the executing satisfaction of various threshold execution criteria is determined, the representation is translated into a second corresponding instance of the compiled workflow different from the first corresponding instance. If this translation satisfaction of the various threshold translation criteria is determined, the second corresponding instance of the compiled workflow is executed to complete a second portion of the manufacture of the engineering targets.
1 . A method of implementing one or more compiled workflows 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;
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 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.
2 . The method according to claim 1 , wherein the biological foundry further comprises a transport path configured to accommodate the articulated handling robot.
3 . The method according to claim 1 , wherein the plurality of instruments comprises a bioreactor, a centrifuge, an incubator, a liquid handling robot, a liquid chromatography system, a gas chromatography system, a mass spectrometry system, a microscope, a electrophoresis device, a electroporation device, a clone separation device, a clone selection device, a thermal cycler, a fume hood, a burner, a mill, a cooler, or a combination thereof.
4 . The method according to claim 1 , wherein the plurality of biological foundry operations comprises a capsule deposition operation, a powder deposition operation, a buffer operation, a capsule assembly operation, a quality control operation, or a combination thereof.
5 . The method according to claim 1 , wherein the plurality of biological foundry operations comprises a bioreactor operation, a centrifuge operation, a thawing operation, an enrichment operation, a freezing operation, an incubation operation, an activation operation, or a combination thereof.
6 . The method according to claim 1 , wherein the plurality of workflow operations comprises a collection operation, a sort operation, an edit operation, a culture operation, a quality control operation, a formulate operation, or a combination thereof.
7 . The method according to claim 1 , wherein the plurality of workflow operations is further spatially ordered, thereby forming a spatiotemporally ordered plurality of workflow operations.
8 . The method according to claim 1 , wherein the plurality of heuristic constraints comprises a first heuristic instruction that defines a non-human readable format of the compiled workflow.
9 . The method according to claim 1 , wherein the plurality of workflow operations comprises a plurality of series workflow operations.
10 . The method according to claim 1 , wherein the plurality of workflow operations comprises a plurality of parallel workflow operations.
11 . The method according to claim 1 , wherein the performance score of the first threshold translation criterion comprises a precision of the translating, an accuracy of the translating, a limit of the translating, or a combination thereof.
12 . The method according to claim 1 , wherein the executing (D) and the executing (H) completes the manufacture of the plurality of the engineering targets.
13 . The method according to claim 1 , wherein the first traverse instruction is different from the second traverse instruction.
14 . The method according to claim 1 , wherein the obtaining (A), the translating (B), the determining (C), the executing (D), the determining (E), the translating (F), the determining (G), the executing (H), or a combination thereof is conducted without human interference.
15 . The method according to claim 1 , wherein the plurality of heuristic constraints comprises a privacy policy, an encryption policy, and a manufacture recordation policy.
16 . The method according to claim 1 , wherein the obtaining (A), the translating (B), the determining (C), the executing (D), the determining (E), the translating (F), the determining (G), the executing (H), or a combination thereof is conducted in real time.
17 . The method according to claim 1 , wherein the determining (E) comprises traversing a prior node utilized in the determining (C).
18 . The method of claim 1 , wherein the disruption associated with the condition at the biological foundry comprises a temporary removal of the first instrument from the biological foundry.
19 . 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.
20 . 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.