BioScan: Parameter-Space Exploration of Synthetic Biocircuits Using MEDA Biochips*
Mohamed Ibrahim1, Bhargab B. Bhattacharya2 and Krishnendu Chakrabarty1
1Duke University, Durham, NC, USA
2Indian Statistical Institute, Kolkata, India
ABSTRACT
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 biocircuitregulatory scanning (BRS) assays to explore the large parameterspace 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 ILPbased synthesis method that implements a BRS-assay on a microelectrode dot-array biochip. Simulation results show that BioScan reduces reagent cost and enhances space-filling properties.
