THE RICHNESS AND VERSATILITY of biological systems make them ideally suited to solve some of the world’s most signicant challenges, such as converting cheap, renewable resources into energy-rich molecules; producing high-quality, inexpensive drugs to ght disease; and remediating polluted sites. Over the years, signicant strides have been made in engineering microorganisms to produce fuels, bulk chemicals, and valuable drugs from inexpensive starting materials; to detect and degrade nerve agents as well as less toxic organic pollutants; and to accumulate metals and reduce radionuclides. e components needed to engineer the chemistry inside a microbial cell

are signicantly dierent from those commonly used to overproduce pharmaceutical proteins. Besides gene expression tools to control metabolism and mathematical models to assess metabolic ux, there is a general need for functional genomics tools to assess the impact of metabolic pathways on the host.