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Tabu Search-Based Synthesis of Dynamically Reconfigurable Digital Microfluidic Biochips

Elena Maftei, Paul Pop, Jan Madsen Technical University of Denmark DTU Informatics. Tabu Search-Based Synthesis of Dynamically Reconfigurable Digital Microfluidic Biochips. www.dreamstime.com. Digital Microfluidic Biochip. Biochip created at Duke University. Microfluidic Biochips.

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Tabu Search-Based Synthesis of Dynamically Reconfigurable Digital Microfluidic Biochips

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  1. Elena Maftei, Paul Pop, Jan MadsenTechnical University of Denmark DTU Informatics Tabu Search-Based Synthesis of Dynamically Reconfigurable Digital Microfluidic Biochips www.dreamstime.com

  2. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Digital Microfluidic Biochip Biochip created at Duke University

  3. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs 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 • Types: • Continuous flow microfluidic biochips • Digital microfluidic biochips

  4. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Microfluidic Biochips • Advantages: • High throughput (reduced sample / reagent consumption)‏ • Space (miniaturization)‏ • Time (parallelism)‏ • Automation (minimal human intervention)‏ • Challenges: • Design complexity • Radically different design and test methods required

  5. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Outline • Motivation • Architecture • Typical Design Tasks • Problem Formulation • Proposed Solution • Tabu Search-Based Synthesis • Dynamic Placement Algorithm • Experimental Evaluation • Conclusions

  6. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Architecture and Working Principles Biochip architectureCell architecture • Electrowetting-on-dielectric • Operations: • Dispensing • Transport • Mixing • Splitting • Storage

  7. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Architecture and Working Principles Biochip architectureCell architecture • Electrowetting-on-dielectric • Operations: • Dispensing • Transport • Mixing • Splitting • Storage

  8. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Architecture and Working Principles Biochip architectureCell architecture • Electrowetting-on-dielectric • Operations: • Dispensing • Transport • Mixing • Splitting • Storage

  9. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Design Tasks Time(s)‏ Operation Area(cells)‏ 10 5 8 3 2x2 1x3 1x3 2x5 Mixing Mixing Dilution Dilution

  10. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Design Tasks Allocation Time(s)‏ Operation Area(cells)‏ 10 5 8 3 2x2 1x3 1x3 2x5 Mixing Mixing Dilution Dilution

  11. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Design Tasks Allocation Time(s)‏ Operation Area(cells)‏ 10 5 8 3 2x2 1x3 1x3 2x5 Mixing Mixing Dilution Dilution Binding & Scheduling

  12. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Design Tasks Allocation Time(s)‏ Operation Area(cells)‏ 10 5 8 3 2x2 1x3 1x3 2x5 Mixing Mixing Dilution Dilution Placement & Routing Binding & Scheduling

  13. Reconfigurability Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs

  14. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs

  15. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs

  16. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs

  17. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs

  18. Reconfigurability Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs

  19. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs

  20. Reconfigurability Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs

  21. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs

  22. Reconfigurability Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs

  23. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Reconfigurability

  24. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Reconfigurability

  25. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Reconfigurability

  26. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Reconfigurability

  27. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Reconfigurability

  28. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Reconfigurability

  29. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Reconfigurability

  30. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Reconfigurability

  31. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Reconfigurability

  32. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Reconfigurability

  33. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Reconfigurability

  34. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Reconfigurability

  35. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Reconfigurability Constraint on the overhead brought by droplet routing.

  36. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Reconfigurability

  37. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Reconfigurability

  38. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Reconfigurability

  39. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Reconfigurability Without dynamic reconfiguration: t+18

  40. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Problem Formulation • Input • Sequencing graph • Library of modules • Area constraint • Output • Implementation which minimizes application execution time • Allocation of modules from modules library • Binding of modules to operations in sequencing graph • Scheduling of operations • Placement of modules on the array

  41. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Related Work • F. Su and K. Chakrabarty. 2005. Unified high-level synthesis and module placement for defect-tolerant microfluidic biochips. In Proceedings of Design Automation Conference. 825-830. • P.-H. Yuh, C.-L. Yang and Y.-W. Chang. 2007.Placement of defect-tolerant digital microfluidic biochips using the T-tree formulation. ACM Journal on Emerging Technologies in Computing Systems 3(3).

  42. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Related Work • F. Su and K. Chakrabarty. 2005. Unified high-level synthesis and module placement for defect-tolerant microfluidic biochips. In Proceedings of Design Automation Conference. 825-830. • P.-H. Yuh, C.-L. Yang and Y.-W. Chang. 2007.Placement of defect-tolerant digital microfluidic biochips using the T-tree formulation. ACM Journal on Emerging Technologies in Computing Systems 3(3). These works consider fixed modules for all operations.

  43. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Optimisation Strategy • Design Optimisation: • Allocation of modules from the library • Binding of modules to operations • Priorities of operations • Schedule of the operations • Placement of modules is performed inside scheduling • Placement of the modules • Algorithm proposed for DR-FPGAs • Free space manager that divides the free space into rectangles • Search engine that selects the best empty rectangle • We have modified MER in order to minimise the fragmentation of free space on the chip Tabu Search List Scheduling MER (Maximal Empty Rectangles)

  44. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs

  45. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Dynamic Placement Algorithm

  46. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Dynamic Placement Algorithm

  47. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Dynamic Placement Algorithm

  48. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Dynamic Placement Algorithm

  49. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Experimental Evaluation • TS Algorithm implemented in Java • 3 set of tests • Quality of the proposed algorithm • Comparison with an Integer Linear Programming (ILP) approach • Improvement brought by dynamic reconfiguration • Comparison between complete TS algorithm and the same algorithm without considering dynamic reconfiguration • Comparison with the approach proposed by Yuh et al.

  50. Tabu Search-Based Synthesis of Dynamically Reconfigurable DMBs Experimental Results Quality of the solution: comparison with an ILP Implementation PCR In Vitro Diagnosis

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