Biochemical Application Modeling

Abstract

This chapter presents the models we use for biochemical applications. We give an informal presentation of the syntax and semantics of the high-level protocol language and define the biochemical application model used in the book. The purpose of the high-level protocol language is to describe biochemical assays in a precise and unambiguous way to allow automatic extraction of the biochemical application. The biochemical application model represents the microfluidic operations of an assay and their interdependencies in terms of input and output relations. We first present a high-level protocol language called Aqua, which serves as the basis for the high-level language we consider in this book. Then, we present a sequencing graph model that captures the behavior of the biochemical protocol. Each node in the graph represents an operation and the edges represent fluid transport. The next chapter presents how the high-level language is compiled into the graph representation. The graph model is used as an input to several of the design tasks addressed in the book.