Virtualizing Existing Fluidic Programs

IF 2.1 4区计算机科学 Q3 COMPUTER SCIENCE, HARDWARE & ARCHITECTURE

ACM Journal on Emerging Technologies in Computing Systems Pub Date : 2023-06-21 DOI:https://dl.acm.org/doi/10.1145/3558550

Caleb Winston, Max Willsey, Luis Ceze

引用次数: 0

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.

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虚拟化现有的流体程序

流体自动化，通过程序化操作小流体来执行实验室规程的实践，极大地提高了生物学家和化学家的工作效率。大多数流体程序，通常被称为协议，是使用api编写的，通过引用设备上的物理位置将协议耦合到特定的硬件。这种耦合使得隔离变得不可能，从而妨碍了可移植性、并发执行和同一设备上协议的组合。我们提出了一种无需修改即可在单个运行时系统之上虚拟化现有流体协议的系统。我们的系统为每个正在运行的协议提供了一个孤立的设备视图，允许它假设它对硬件有唯一的访问权限。我们提供了一个概念验证实现，它可以并发地执行和组合使用流行的Opentrons Python API编写的协议。与串行执行相比，并发执行实现了接近线性的加速，因为协议花费了大量时间等待。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

ACM Journal on Emerging Technologies in Computing Systems 工程技术-工程：电子与电气

CiteScore

4.80

自引率

4.50%

发文量

审稿时长

3 months

期刊介绍： The Journal of Emerging Technologies in Computing Systems invites submissions of original technical papers describing research and development in emerging technologies in computing systems. Major economic and technical challenges are expected to impede the continued scaling of semiconductor devices. This has resulted in the search for alternate mechanical, biological/biochemical, nanoscale electronic, asynchronous and quantum computing and sensor technologies. As the underlying nanotechnologies continue to evolve in the labs of chemists, physicists, and biologists, it has become imperative for computer scientists and engineers to translate the potential of the basic building blocks (analogous to the transistor) emerging from these labs into information systems. Their design will face multiple challenges ranging from the inherent (un)reliability due to the self-assembly nature of the fabrication processes for nanotechnologies, from the complexity due to the sheer volume of nanodevices that will have to be integrated for complex functionality, and from the need to integrate these new nanotechnologies with silicon devices in the same system. The journal provides comprehensive coverage of innovative work in the specification, design analysis, simulation, verification, testing, and evaluation of computing systems constructed out of emerging technologies and advanced semiconductors