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Recently, global biomass-burning research has grown from what was primarily a climate field to include a vibrant air quality observation and forecasting community. While new fire monitoring systems are based on fundamental Earth Systems Science (ESS) research, adaptation to the forecasting problem requires special procedures and simplifications. In a reciprocal manner, results from the air quality research community have contributed scientifically to basic ESS. To help exploit research and data products in climate, ESS, meteorology and air quality biomass burning communities, the joint Navy, NASA, NOAA, and University Fire Locating and Modeling of Burning Emissions (FLAMBE) program was formed in 1999. Based upon the operational NOAA/NESDIS Wild-Fire Automated Biomass Burning Algorithm (WF_ABBA) and the near real time University of Maryland/NASA MODIS fire products coupled to the operational Navy Aerosol Analysis and Prediction System (NAAPS) transport model, FLAMBE is a combined ESS and operational system to study the nature of smoke particle emissions and transport at the synoptic to continental scales. In this paper, we give an overview of the FLAMBE system and present fundamental metrics on emission and transport patterns of smoke. We also provide examples on regional smoke transport mechanisms and demonstrate that MODIS optical depth data assimilation provides significant variance reduction against observations. Using FLAMBE as a context, throughout the paper we discuss observability issues surrounding the biomass burning system and the subsequent propagation of error. Current indications are that regional particle emissions estimates still have integer factors of uncertainty.