Application Mapping and Simulation

Abstract

In this chapter we address the problem of mapping a biochemical application modeled as a sequencing graph to a given biochip architecture. The mapping consists of the binding, scheduling, and routing tasks. We first propose a constraint programming (CP) synthesis approach that optimally synthesizes a biochemical application onto the specified biochip architecture with the application completion time minimization as the target objective. The synthesis process involves performing binding and scheduling of operations while satisfying the dependency and resource constraints. Our CP approach ignores fluid routing. We also propose a computationally efficient heuristic approach that also takes into account fluidic routing (contention aware edge scheduling) together with the operation mapping. Real-life case studies and a set of synthetic benchmarks have been synthesized on different architectures for validating the proposed approach. To aid the development and testing during the application development phase, we have also developed a simulator that shows how a given mapped biochemical application is executed on a target biochip architecture. The proposed approaches are expected to reduce human effort, enabling designers to take early design decisions by being able to evaluate their proposed architecture, minimizing the design cycle time and also facilitating programmability and automation.