Biochemical network reconstructions represent valuable tools for the computational metabolic modeling of organisms that present a great biotechnological interest. An in silico multi-compartmental model of the central metabolism of the plant Brassica napus (Rapeseed) was constructed, aiming to investigate the metabolic properties of the Brassicaceae family. This family comprises many plants with major importance for the energy and nutrition sector, including the model plant Arabidopsis thaliana. The model utilized as objective function to be subsequently optimized, the biomass production of rapeseed developing embryos, which are characterized by a very high, oil content, up to 60% of biomass weight. In order to study global network properties of seed metabolism, various methods were employed, like Flux Balance Analysis, Principal Component Analysis of the flux space and reaction deletion studies, which simulate the effect of gene knock-out experiments. The model successfully simulated seed growth during the stage of oil accumulation and provided insight, regarding certain aspects of network plasticity, with the emphasis given in lipid biosynthesis regulation. Biotechnol. Bioeng. 2011; 108: 1673-1682. (C) 2011 Wiley Periodicals, Inc.