Automatic synthesis of microfluidic large scale integration chips from a domain-specific language

Abstract

Abstract-BioCoder is a domain-specific language by which chemists and biologists can express experimental protocols in a manner that is unambiguous and clearly repeatable. This paper presents a software toolchain that converts a protocol specified in a restricted subset of BioCoder to a technology-specific description of the protocol, targeting flow-based microfluidic large-scale integration (mLSI) chips. The technology-specific description can then be used to either: (1) execute the protocol on a capable chip; or (2) to derive the architecture of a new mLSI chip that can execute the protocol.

Flow-Layer Physical Design for Microchips Based on Monolithic Membrane Valves

“…This article focuses on the flow-layer physical-design stage. Our future work will be integrating the control synthesis and physical design from [5] and [7].…”

“…In our framework, a biological experiment is specified using a domain-specific language suitable for the chosen technology; architectural synthesis, which includes scheduling, resource allocation, and binding steps, converts this specification into a graphbased netlist (plumbing network) capable of executing the experiment [7], [9]. If desired, the netlist can be converted to the microfluidic hardware description language (MHDL), which is human readable representation.…”

Simulated annealing-based placement for microfluidic large scale integration (mLSI) chips

“…By limiting the number of control inputs introduced due to post-routing fluid channel intersections the length of the longest fluid channels could be taken into consideration as a secondary criteria for optimization. Prior work on mLSI CAD includes application mapping [9,14], architectural synthesis [10], control synthesis [2, 4 11], hardware design languages [6,7], and testing [5]; however, these papers do not address mLSI physical design.…”

“…Automation would be beneficial, as schematic drawing is tedious, non-scalable, and error-prone. mLSI chips may be specified using domain-appropriate hardware design languages in the near future [6], and high-level synthesis tools that convert biochemical protocol specifications into protocolspecific mLSI chips are within reach [7]. It should be possible to leverage techniques from semiconductor VLSI/CAD to automate the design and layout process for mLSI chips.…”

An end-to-end solution for automation of biological protocols

“…Wires are substituted by channels between chambers, and logic gates (and timing elements) are supplanted by chambers. A simulator is also integrated with the basic compiler which validates the design by verifying the connections between elements and the pressure inside the channels and chambers 61,62 . AquaCore IDE is an environment for implementing biological protocols on a microfluidic device.…”