Date: Thursday 30 March 2017
Time: 16:00 - 17:30
Location / Room: Exhibition Theatre
Organisers:
Paul Pop, Technical University of Denmark, DK
Seetal Potluri, Technical University of Denmark, DK
Chair:
Jan Madsen, Technical University of Denmark, DK
Co-Chair:
Seetal Potluri, Technical University of Denmark, DK
Microfluidic biochips (also called lab-on-a-chip) are replacing the conventional biochemical analyzers by integrating all the necessary functions for biochemical analysis using microfluidics. The current trend is towards cyberphysical biochip platforms that integrate novel sensors and actuators, as well as on-chip control circuits. Motivated by the similarity to microelectronics, researchers have started to propose EDA tools for the synthesis of microfluidic biochips. However, we advocate for a paradigm shift, to bridge the formidable barrier that separates engineering (or chip design) from practical biochemistry and microbiology. The special session will serve as a "call to arms" for more focused and relevant research to increase the adoption of microfluidics in translational research.
| Time | Label | Presentation Title Authors |
|---|---|---|
| 16:00 | 12.8.1 | DIGITAL-MICROFLUIDIC BIOCHIPS FOR QUANTITATIVE ANALYSIS: BRIDGING THE GAP BETWEEN MICROFLUIDICS AND MICROBIOLOGY Speaker: Krishnendu Chakrabarty, Duke University, US Authors: Mohamed Ibrahim and Krishnendu Chakrabarty, Duke University, US Abstract Digital-microfluidics technology has shown considerable promise for advancing sample preparation and point-of-care diagnostics; therefore, it has the potential to transform microbiology and biochemistry research. Over the past decade, a number of microfluidics design-automation techniques have been developed for on-chip droplet manipulation. However, these methods overlook the myriad complexities of biomolecular protocols and they have yet to make a significant impact in biochemistry/microbiology research. A paradigm shift in biochip design automation and a ``phase transition'' in research are clearly needed to bridge this gap between microfluidics and microbiology. In this paper, we explain how researchers from design-automation and embedded systems can play a key role in this transition. We present a new synthesis flow that uses realistic models of biomolecular protocols and cyberphysical adaptation to address real-world microbiology applications. We also present a list of metrics that can be used for the assessment of design-automation techniques for microbiology applications. Download Paper (PDF; Only available from the DATE venue WiFi) |
| 16:30 | 12.8.2 | THE CASE FOR SEMI-AUTOMATED DESIGN OF MVLSI BIOCHIPS Speaker: Jeffrey McDaniel, University of California, Riverside, US Authors: Jeffrey McDaniel, William H. Grover and Philip Brisk, University of California, Riverside, US Abstract In recent years, significant interest has emerged in the problem of fully automating the design of microfluidic very large scale integration (mVLSI) chips, a popular class of Lab-on-a-Chip (LoC) devices that can automatically execute a wide variety of biological assays. To date, this work has been carried out with little to no input from LoC designers. We conducted interviews with approximately 100 LoC designers, biologists, and chemists from academia and industry; uniformly, they expressed frustration with existing design solutions, primarily commercially available software such as AutoCAD and Solidworks; however, they expressed limited interest and considerable skepticism about the potential for "push-button" end-to-end automation. In response, we have developed a semi-automated mVLSI drawing tool that is designed specifically to address the pain points elucidated by our interviewees. We have used this tool to rapidly reproduce several previously published LoC architectures and generate fabrication ready specifications. Download Paper (PDF; Only available from the DATE venue WiFi) |
| 17:00 | 12.8.3 | SYNTHESIS OF ON-CHIP CONTROL CIRCUITS FOR MVLSI BIOCHIPS Speaker: Seetal Potluri, Technical University of Denmark, DK Authors: Seetal Potluri1, Alexander Schneider2, Martin Hørslev-Petersen2, Paul Pop2 and Jan Madsen2 1Xilinx Asia Pacific, SG; 2Technical University of Denmark, DK Abstract Microfluidic VLSI (mVLSI) biochips help perform biochemistry at miniaturized scales, thus enabling cost, performance and other benefits. Although biochips are expected to replace biochemical labs, including point-of-care devices, the off-chip pressure actuators and pumps are bulky, thereby limiting them to laboratory environments. To address this issue, researchers have proposed methods to reduce the number of off-chip pressure sources, through integration of on-chip pneumatic control logic circuits fabricated using three-layer monolithic membrane valve technology. Traditionally, mVLSI biochip physical design was performed assuming that all of the control logic is off-chip. However, the problem of mVLSI biochip physical design changes significantly, with introduction of on-chip control, since along with physical synthesis, we also need to (i) perform on/off-chip control partitioning, (ii) on-chip control circuit design and (iii) the integration of on-chip control in the placement and routing design tasks. In this paper we present a design methodology for logic synthesis and physical synthesis of mVLSI biochips that use on-chip control. We show how the proposed methodology can be successfully applied to generate biochip layouts with integrated on-chip pneumatic control. Download Paper (PDF; Only available from the DATE venue WiFi) |
| 17:15 | 12.8.4 | SCHEDULING AND OPTIMIZATION OF GENETIC LOGIC CIRCUITS ON MICROFLUIDIC BIOCHIPS Speaker: Tsung-Yi Ho, National Tsing Hua University, TW Authors: Yu-Jhih Chen1, Sumit Sharma2, Sudip Roy3 and Tsung-Yi Ho1 1National Tsing Hua University, TW; 2Indian Institute of Technology Roorkee, IN; 3IIT Roorkee, IN Abstract Synthetic biologists design genetic logic circuit using living cells. A challenge in this task is the difficulty in constructing bigger logic circuits with several living cells due to the crosstalk effect among the biological cells. In order to remove the crosstalk effect, current practice is to use separate chambers on a flow-based microfluidic biochip to isolate each reaction zone. The state-of-the-art technique assumes different reaction times for each gates in a genetic logic circuit. This assumption is pessimistic as each gate has different reaction rate from others. Hence, it will cause unnecessary waiting time for faster gates and this may in turn increase the total experiment completion time significantly. In this paper, we propose a genetic logic circuit synthesis technique for flow-based microfluidic biochip considering different reaction time of each logic gate. Simulation results show that the proposed scheme reduces the total experiment completion time. We further minimize the number of control valves and optimize the routing of flow and control layers in the chip layout, which in turn reduces the design cost. Download Paper (PDF; Only available from the DATE venue WiFi) |
| 17:30 | End of session | |