BioScan: Parameter-Space Exploration of Synthetic Biocircuits Using MEDA Biochips

摘要

Recent advances in microfluidic technology offer efficient platforms to emulate complex molecular networks of biological pathways (biocircuits) on a lab-on-chip. The behavior of biocircuits is governed by a number of gene-regulatory parameters. A fundamental challenge in synthesizing and verifying biocircuits is the lack of design tools that implement biocircuit-regulatory scanning (BRS) assays to explore the large parameter-space efficiently, while optimizing synthesis time and reagent cost. In this paper, we introduce an optimization flow named BioScan for systematic exploration of the parameter-space of a biocircuit. BioScan includes: (1) a statistical approach to determine a subset of mixing ratios of reagents that span the entire parameter space as densely as possible under cost constraints; (2) an ILP-based synthesis method that implements a BRS-assay on a micro-electrode dot-array biochip. Simulation results show that BioScan reduces reagent cost and enhances space-filling properties.