Virtualizing Existing Fluidic Programs

@article{10.1145/3558550,
  author = {Winston, Caleb and Willsey, Max and Ceze, Luis},
  title = {Virtualizing Existing Fluidic Programs},
  year = {2022},
  publisher = {Association for Computing Machinery},
  address = {New York, NY, USA},
  issn = {1550-4832},
  url = {https://doi.org/10.1145/3558550},
  doi = {10.1145/3558550},
  journal = {Journal on Emerging Technologies in Computing Systems},
  month = {jul},
  keywords = {cloud lab, pipetting robots, virtualization, protocols, fluidics, biofoundry}
}

Abstract

Fluidic automation, the practice of programmatically manipulating small fluids to execute laboratory protocols, has led to vastly increased productivity for biologists and chemists. Most fluidic programs, commonly referred to as protocols, are written using APIs that couple the protocol to specific hardware by referring to the physical locations on the device. This coupling makes isolation impossible, preventing portability, concurrent execution, and composition of protocols on the same device.

We propose a system for virtualizing existing fluidic protocols on top of a single runtime system without modification. Our system presents an isolated view of the device to each running protocol, allowing it to assume it has sole access to hardware. We provide a proof-of-concept implementation that can concurrently execute and compose protocols written using the popular Opentrons Python API. Concurrent execution achieves near-linear speedup over serial execution since protocols spend much of their time waiting.