Routing-Based Synthesis of Digital Microfluidic Biochips Elena Maftei, Paul Pop, Jan Madsen Technical University of Denmark CASES’101Routing-Based Synthesis of Digital Microfluidic Biochips

Microfluidic Biochips CASES’102Routing-Based Synthesis of Digital Microfluidic Biochips Technical Univ. of Denmark 2010 Duke University 2002 Continuous-flow biochips Droplet-based biochips

Microfluidic Biochips  Applications  Sampling and real time testing of air/water for biochemical toxins  Detection of adverse atmospheric conditions  DNA analysis and sequencing  Clinical diagnosis  Point of care devices  Advantages:  High throughput (reduced sample / reagent consumption)‏  Space (miniaturization)‏  Time (parallelism)‏  Automation (minimal human intervention)‏ CASES’103Routing-Based Synthesis of Digital Microfluidic Biochips

Outline  Motivation  Architecture  Typical Design Tasks  Problem Formulation  Proposed Solution  GRASP-Based Synthesis  Experimental Evaluation  Conclusions CASES’104Routing-Based Synthesis of Digital Microfluidic Biochips

Biochip Architecture Biochip created at Duke University CASES’105Routing-Based Synthesis of Digital Microfluidic Biochips

Electrowetting on Dielectric CASES’106Routing-Based Synthesis of Digital Microfluidic Biochips

Module-Based Synthesis: Design Tasks Scheduling Binding Placement Allocation CASES’107Routing-Based Synthesis of Digital Microfluidic Biochips

Module-Based Synthesis CASES’108Routing-Based Synthesis of Digital Microfluidic Biochips

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Module-Based Synthesis CASES’1014Routing-Based Synthesis of Digital Microfluidic Biochips

Mixing  Droplets can move anywhere  Fixed area: module-based synthesis  Unconstrained: routing-based synthesis CASES’1015Routing-Based Synthesis of Digital Microfluidic Biochips

Routing-Based Synthesis CASES’1016Routing-Based Synthesis of Digital Microfluidic Biochips

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When will the operations complete?  For module-based synthesis we know the completion time from the module library.  But now there are no modules, the droplets can move anywhere.  How can we find out the operation completion times? CASES’10Routing-Based Synthesis of Digital Microfluidic Biochips28

Characterizing operations  If the droplet does not move: very slow mixing by diffusion  If the droplet moves, how long does it take to complete?  Mixing percentages: p 0, p 90, p 180 ? CASES’1029Routing-Based Synthesis of Digital Microfluidic Biochips

Characterizing operations  We know how long an operation takes on modules  Starting from this, can determine the percentages? CASES’1030Routing-Based Synthesis of Digital Microfluidic Biochips

Decomposing modules Safe, conservative estimates p 90 =0.1%, p 180 =-0.5%, p 0 =0.29% and 0.58% CASES’1031Routing-Based Synthesis of Digital Microfluidic Biochips Moving a droplet one cell takes 0.01 s.

Routing-Based Synthesis CASES’1032Routing-Based Synthesis of Digital Microfluidic Biochips

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Droplet- vs. Module-Based Synthesis Module-Based SynthesisRouting-Based Synthesis CASES’1034Routing-Based Synthesis of Digital Microfluidic Biochips

Problem Formulation  Input  Application graph  Architecture (matrix of electrodes)  Library of non-reconfigurable devices  Output  Implementation which minimizes application execution time  Droplet routes for all reconfigurable operations  Allocation and binding of non-reconfigurable modules from a library  Scheduling of operations CASES’1035Routing-Based Synthesis of Digital Microfluidic Biochips

Proposed Solution CASES’1036Routing-Based Synthesis of Digital Microfluidic Biochips

Proposed Solution Meet Execute CASES’1037Routing-Based Synthesis of Digital Microfluidic Biochips

Proposed Solution Meet Execute Minimize the time until the droplet(s) arrive at destination Minimize the completion time for the operation CASES’1038Routing-Based Synthesis of Digital Microfluidic Biochips

GRASP-Based Heuristic  Greedy Randomized Adaptive Search Procedure CASES’1039Routing-Based Synthesis of Digital Microfluidic Biochips

GRASP-Based Heuristic  Greedy Randomized Adaptive Search Procedure CASES’1040Routing-Based Synthesis of Digital Microfluidic Biochips

GRASP-Based Heuristic  Greedy Randomized Adaptive Search Procedure For each droplet: Determine possible moves Evaluate possible moves Make a list of best N possible moves Perform a randomly chosen possible move CASES’1041Routing-Based Synthesis of Digital Microfluidic Biochips

GRASP-Based Heuristic Greedy Randomized Adaptive Search Procedure For each droplet: Determine possible moves Evaluate possible moves Make a list of best N possible moves Perform a randomly chosen possible move CASES’1042Routing-Based Synthesis of Digital Microfluidic Biochips

GRASP-Based Heuristic Greedy Randomized Adaptive Search Procedure For each droplet: Determine possible moves Evaluate possible moves Make a list of best N possible moves Perform a randomly chosen possible move CASES’1043Routing-Based Synthesis of Digital Microfluidic Biochips

GRASP-Based Heuristic Greedy Randomized Adaptive Search Procedure For each droplet: Determine possible moves Evaluate possible moves Make a list of best N possible moves Perform a randomly chosen possible move CASES’1044Routing-Based Synthesis of Digital Microfluidic Biochips

GRASP-Based Heuristic Greedy Randomized Adaptive Search Procedure For each droplet: Determine possible moves Evaluate possible moves Make a list of best N possible moves Perform a randomly chosen possible move CASES’1045Routing-Based Synthesis of Digital Microfluidic Biochips

Experimental Evaluation Routing-Based Synthesis (RBS) vs. to Module-Based Synthesis* (MBS) Two real-life applications (the table below) Ten synthetic benchmarks (see the paper) (*) E. Maftei at al.: Tabu Search-Based Synthesis of Dynamically Reconfigurable Digital Microfluidic Biochips. CASES, 2009 (best paper award) CASES’1046Routing-Based Synthesis of Digital Microfluidic Biochips

Contributions and Message  Message  Labs-on-a-chip can be implemented with microfluidics  CAD tools are essential for the design of biochips  Contributions  Eliminated the concept of “virtual modules” and proposed a routing-based synthesis approach  Proposed a GRASP-based algorithm for showing that routing- based synthesis leads to significant improvements compared to module-based synthesis CASES’1047Routing-Based Synthesis of Digital Microfluidic Biochips

Discussion  Module-based vs. routing-based  Module-based needs an extra routing step between the modules; Routing-based performs unified synthesis and routing  Module-based wastes space: only one module-cell is used; Routing-based exploits better the application parallelism  Module-base can contain the contamination to a fixed area;  We are extending routing-based to consider contamination  Module-based: nice, useful abstraction?  Routing based: too much spaghetti? CASES’10Routing-Based Synthesis of Digital Microfluidic Biochips48