Karr, Sanghvi, et al. (2012) propose a whole-cell computational model for predicting phenotype from genotype in Mycoplasma genitalium. Their model simulates myriad cell processes such as DNA replication, RNA transcription and regulation, protein synthesis, metabolism and cell division at the molecular level over the life-cycle of the organism.
They achieve this by combining many existing mathematical and computational models into one piece of software. The article suggests that this is the first comprehensive whole-cell model at the molecular level in detail. They cite previous molecular-level models for their sub-modules, but don't go on to discuss more coarse-grained genotype-to-phenotype models. Their model is exciting, but the 10 hours of simulation on a top-end computer cluster to follow the life-cycle of a single organism is unreasonable for someone who wants to study evolutionary processes.
Are there prior reasonably accurate computational (or even better, analytic) genotype-to-phenotype models? If there are, what are some of the best coarse-grained genotype-to-phenotype models for commonly studied organisms such as E.Coli?