Automated genome annotation and metabolic model reconstruction in the SEED and Model SEED

Over the past decade, genome-scale metabolic models have proven to be a crucial resource for predicting organism phenotypes from genotypes. These models provide a means of rapidly translating detailed knowledge of thousands of enzymatic processes into quantitative predictions of whole-cell behavior. Until recently, the pace of new metabolic model development was eclipsed by the pace at which new genomes were being sequenced. To address this problem, the RAST and the Model SEED framework were developed as a means of automatically producing annotations and draft genome-scale metabolic models. In this chapter, we describe the automated model reconstruction process in detail, starting from a new genome sequence and finishing on a functioning genome-scale metabolic model. We break down the model reconstruction process into eight steps: submitting a genome sequence to RAST, annotating the genome, curating the annotation, submitting the annotation to Model SEED, reconstructing the core model, generating the draft biomass reaction, auto-completing the model, and curating the model. Each of these eight steps is documented in detail.