ASPIRE Organic Lab Simulator

A simulation software for organic synthesis on an automated experimentation platform.

Dependencies

• simpy: used for the actual DES
• casymda: used for managing instruction dependencies

Design

The architecture of the simulator is based on the following concepts,

hw.LabObject:

• any physical object except reaction-participating chemicals
• a state machine

hw.Device: a hw.LabObject that

• can, by receiving hw.Instruction, execute its action_methods to
• change its own state
• change other hw.LabObject instances’ states
• move simulation clock

An action_method is always implemented as two separate methods

• PreActor(action_parameters)
  • checks preconditions, error out if not met
  • make projections about the action
  • what hw.LabObjects will be occupied during this action?
  • how long will this action take?
• PostActor(action_parameters)
  • makes state transitions for all involved objects

hw.Instruction:

• carries action_parameters
• knows its preceding/succeeding hw.Instruction instances
• lifecycle
  • when triggered, sends one request for each involved hw.LabObject instance
  • a request returns a place in the queue of that hw.LabObject (first come first serve)
  • once all requests are accepted, run the action’s PreActor
  • move the simulation clock
  • run the action’s PostActor
  • releases all occupied hw.LabObject instances
  • trigger succeeding hw.Instruction instances in its callbacks

JUNIOR demo

A demo of N-Sulfonylation benchmark reaction can be accessed through this temporary link.

The demo simulates the following instructions.