BioScript: programming safe chemistry on laboratories-on-a-chip

Ott, Jason; Loveless, Tyson; Curtis, C. J.; Lesani, Mohsen; Brisk, Philip

doi:10.1145/3276498

Cited by 20 publications

(24 citation statements)

References 113 publications

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“…A compiler or interpreter will translate the specification into an executable format that will run on the SP-LoC. A number of domain-specific programming languages have been proposed for SP-LoCs [4,5,17,18,64,83,84,86]; while most of these languages are tied to specific SP-LoC technologies, any DSL compatible with DMFBs (see § 2.2) could be used as a front-end to the compiler presented here.…”

Section: Language Design For Sp-locsmentioning

confidence: 99%

A performance-optimizing compiler for cyber-physical digital microfluidic biochips

Loveless

Ott

Brisk

2020

Proceedings of the 18th ACM/IEEE International Symposium on Code Generation and Optimization

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This paper introduces a compiler optimization strategy for Software-Programmable Laboratories-on-a-Chip (SP-LoCs), which miniaturize and automate a wide variety of benchtop laboratory experiments. The compiler targets a specific class of SP-LoCs that manipulate discrete liquid droplets on a 2D grid, with cyber-physical feedback provided by integrated sensors and/or video monitoring equipment. The optimization strategy employed here aims to reduce the overhead of transporting fluids between operations, and explores tradeoffs between the latency and resource requirements of mixing operations: allocating more space for mixing shortens mixing time, but reduces the amount of spatial parallelism available to other operations. The compiler is empirically evaluated using a cycle-accurate simulator that mimics the behavior of the target SP-LoC. Our results show that a coalescing strategy, inspired by graph coloring register allocation, effectively reduces droplet transport latencies while speeding up the compiler and reducing its memory footprint. For biochemical reactions that are dominated by mixing operations, we observe a linear correlation between a preliminary result using a default mixing operation resource allocation and the percentage decrease in execution time that is achieved via resizing. CCS Concepts • Computer systems organization → Embedded and cyber-physical systems; Parallel architectures; Reconfigurable computing; • Software and its engineering → Compilers; • Hardware → Emerging languages and compilers; Microelectromechanical systems.

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Section: Language Design For Sp-locsmentioning

confidence: 99%

A performance-optimizing compiler for cyber-physical digital microfluidic biochips

Loveless

Ott

Brisk

2020

Proceedings of the 18th ACM/IEEE International Symposium on Code Generation and Optimization

Self Cite

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“…Other approaches have proposed domain specific languages (DSLs) to increase expressiveness [6,15,20,21,39]. A DSL can support features like data-dependent control flow, which is necessary if a fluidic program is expected to act on the value of a sensor reading.…”

Section: Controlling Dmf Devicesmentioning

confidence: 99%

“…Dynamic interpretation also suffers from sub-optimal place and route, as the system only considers one basic block at a time. Others have proposed static compilers capable of handling control flow, e.g., Curtis et al [15] and Ott et al [39]. These approaches offer a static guarantee that the program (ignoring errors) can be successfully routed, but they are all less expressive than Puddle.…”

Section: Related Workmentioning

confidence: 99%

“…Unlike static approaches to digital microfluidic programming [15,20,39], dynamism also allows for metaprogramming. Users can use features of their favorite languages (reflection, macros, first-class functions, etc.)…”

Section: Benefits Of Dynamismmentioning

confidence: 99%

“…The rich domains in which fluidic systems are used also pose a challenge to programming languages: can we statically reason about the contents of the fluids? Recent work has approached this from a chemical safety perspective, preventing accidental dangerous reactions [39]. At the runtime system level, we hope to incorporate more advanced place and route techniques from the literature into Puddle.…”

Section: Future Workmentioning

confidence: 99%

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Puddle

Willsey

Stephenson

Takahashi

et al. 2019

Proceedings of the Twenty-Fourth International Conference on Architectural Support for Programming Languages and Operating Syst

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Microfluidic devices promise to automate wetlab procedures by manipulating small chemical or biological samples. This technology comes in many varieties, all of which aim to save time, labor, and supplies by performing lab protocol steps typically done by a technician. However, existing microfluidic platforms remain some combination of inflexible, error-prone, prohibitively expensive, and difficult to program. We address these concerns with a full-stack digital microfluidic automation platform. Our main contribution is a runtime system that provides a high-level API for microfluidic manipulations. It manages fluidic resources dynamically, allowing programmers to freely mix regular computation with microfluidics, which results in more expressive programs than previous work. It also provides real-time error correction through a computer vision system, allowing robust execution on cheaper microfluidic hardware. We implement our stack on top of a low-cost droplet microfluidic device that we have developed. We evaluate our system with the fully-automated execution of polymerase chain reaction (PCR) and a DNA sequencing preparation protocol. These protocols demonstrate high-level programs that combine computational and fluidic operations such as input/output of reagents, heating of samples, and data analysis. We also evaluate the impact of automatic error correction on our system's reliability.

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