Systems and methods for supporting multiple automated workflows

A system for implementing workflows comprising a first device, wherein the first device comprises:

• a display;
• a power supply;
• a communications interface;
• one or more peripheral devices including a reagent handling device, the reagent handling device comprising:
• a wash manifold,
• a primary valve that regulates an internal flow path in the reagent handling device,
• a plurality of reagent containers, wherein each reagent container in the plurality of reagent containers comprises a valve that controls a flow from the respective reagent container to the primary valve,
• a sterilization container configured to hold a sterilization fluid, the sterilization container comprising a valve that regulates a flow of the sterilization fluid either to the primary valve or to the wash manifold,
• the wash manifold is coupled to the respective valve of each reagent container in the plurality of reagent containers, wherein the wash manifold regulates the flow of the sterilization fluid from the sterilization container to the plurality of reagent containers, and
• a dispense manifold that is coupled to the primary valve and comprises a plurality of dispensers, the dispense manifold configured to control a flow from the primary valve to the plurality of dispensers;
• one or more processors;
• memory;
• and
• one or more programs, wherein the one or more programs are stored in the memory and are configured to be executed by the one or more processors, the one or more programs including instructions for:
• (A) obtaining, in electronic form, a first plurality of organic engineering targets;
• (B) assigning the first plurality of organic engineering targets to a first uncompiled workflow, wherein
• the first uncompiled workflow is configured to produce the first plurality of organic engineering targets,
• the first uncompiled workflow comprises a branch condition, a loop condition, or a nested condition,
• the first uncompiled workflow is associated with a first subset of process modules in a plurality of process modules,
• each respective process module in the plurality of process modules is associated with a different subset of unit operation definitions in a plurality of unit operation definitions,
• each respective unit operation definition in the plurality of unit operation definitions is independently associated with a corresponding time interval, and
• each respective unit operation definition in the plurality of unit operation definitions is independently associated with a first subset of instruments in a plurality of instruments;
• (C) translating, for each respective organic engineering target in the first plurality of organic engineering targets, the first uncompiled workflow into a corresponding instance of a compiled first workflow for the respective organic engineering target using a transport path without human input, wherein the corresponding instance of the compiled first workflow comprises:
• (i) for each respective instrument in the first subset of instruments:
• (a) an address of the respective instrument comprising:
• a coarse grain address of the respective instrument that is associated with a marker of the respective instrument configured to provide positional information to localize a transporter, wherein an articulated handling robot is attached to the transporter, and
• (b) one or more execution instructions comprising:
• a logical dependency of one or more unit operations of the compiled workflow defining procedures for processing samples,
• a coarse traverse instruction that commands the transporter to traverse to the respective marker of the respective instrument, and
• a fine traverse instruction that commands the articulated handling robot to move to at least one spatial coordinate associated with the respective instrument, and
• (ii) a first plurality of unit operations, wherein the first plurality of unit operations is temporally organized into a linear temporal order by resolving the branch condition, the loop condition, or the nested condition based on a value associated with the branch condition, the loop condition, or the nested condition, and wherein, each respective unit operation in the first plurality of unit operations is characterized by the time interval of the corresponding unit operation definition,
• thereby forming a plurality of instances of the compiled first workflow.

A method of implementing one or more workflows:

• at a device comprising one or more processors, memory storing one or more programs for execution by the one or more processors, a controller, a plurality of instruments including a multi-well plate centrifuge instrument, a communications interface in electrical communication with at least the plurality of instruments, and a power supply;
• the one or more programs singularly or collectively using the one or more processors to execute a method comprising:
• (A) obtaining in electronic form, a first plurality of organic engineering targets;
• (B) assigning, via the controller, the first plurality of organic engineering targets to a first uncompiled workflow, wherein
• the first uncompiled workflow is configured to produce each organic engineering target in the first plurality of organic engineering targets in a corresponding well in a plate in a first set of multi-well plates,
• the first uncompiled workflow comprises a branch condition, a loop condition, or a nested condition,
• the first uncompiled workflow is associated with a first subset of process modules in a plurality of process modules,
• each respective process module in the plurality of process modules is associated with a different subset of unit operation definitions in a plurality of unit operation definitions,
• each respective unit operation definition in the plurality of unit operation definitions is independently associated with a corresponding time interval, and
• each respective unit operation definition in the plurality of unit operation definitions is independently associated with a first subset of instruments in the plurality of instruments, wherein the first subset of instruments includes the multi-well plate centrifuge instrument;
• and
• (C) translating, via the controller, for each respective organic engineering target in the first plurality of organic engineering targets, the first uncompiled workflow into a corresponding instance of a compiled first workflow for the respective organic engineering target using a transport path without human input, wherein the corresponding instance of the compiled first workflow comprises:
• (i) for each respective instrument in the first subset of instruments (a) an address of the respective instrument, and (b) one or more execution instructions, wherein the one or more execution instructions for a multi-well plate centrifuge instrument comprise:
• b.i) determining a mass of each multi-well plate in a first set of multi-well plates,
• b.ii) disposing each multi-well plate in the first set of multi-well plates into the multi-well plate centrifuge instrument,
• b.iii.1) obtaining a set of counter balances corresponding to the first set of multi-well plates,
• b.iii.2) disposing each respective counter balance in the multi-well plate centrifuge instrument at a position opposite the corresponding multi-well plate in the first set of multi-well plates,
• b.iii) adjusting, without human intervention, a mass of each respective counter balance in the set of counter balances to be equal to the corresponding multi-well plate in the first set of multi-well plates, and
• b.iv) operating the multi-well centrifuge instrument, and
• (ii) a first plurality of unit operations, wherein the first plurality of unit operations is temporally organized into a linear temporal order by resolving the branch condition, the loop condition, or the nested condition based on a value associated with the branch condition, the loop condition, or the nested condition, and wherein each respective unit operation in the first plurality of unit operations is characterized by the time interval of the corresponding unit operation definition,
• thereby forming a plurality of instances of the compiled first workflow.