An automated microfluidic cell culture platform that creates and maintains independently programmable diffusion-based gradients is reported. Temporal modulation of the source and sink flow patterns allow generation of extremely stable spatial gradients. We developed a system that integrates 30 parallel gradients in a single device, with 10 different chemical formulations and 3 replicates. Mammalian fibroblast and macrophage cells were screened for NFκB pathway activity under gradients of TNFα, PDGF, and LPS, and multiparameter measurements were performed to demonstrate the capability of the device in dynamic single-cell analysis.