We introduce an online synthesis flow, focusing primarily on the virtual topology and operation binder, for digital microfluidic biochips, which will enable real-time response to errors and control flow. The objective of this flow is to facilitate fast assay synthesis while minimally compromising the quality of results. In particular, we show that a virtual topology, which constrains the allowable locations of assay operations such as mixing, dilution, sensing, etc., in lieu of traditional placement, can significantly speed up the synthesis process without significantly lengthening assay execution time. We present a base virtual topology and show how it can be leveraged to reduce algorithmic runtimes and guarantee rout ability. We later present several variations of the virtual topology and present experimental results demonstrating best-design practices. We present two binding solutions. The first is a left-edge binding algorithm, while the second is a more intelligent path-based binding algorithm that leverages spatial and temporal locality to produce superior results. © 2013 IEEE.