Lecture 1: An Introduction to Whole-Cell Modeling
Whole-cell (WC) computational models that predict phenotype from genotype are needed to help bioengineers rationally design bacteria and other organisms. Despite their potential, numerous challenges remain to achieve WC models. We do not yet have all of the data need for WC modeling; the data that is available for WC modeling is heterogeneous and scattered across the literature; we have few tools for scalably designing, simulating, calibrating, and validating models; and few published models are composable. Nevertheless, we and others recently demonstrated the feasibility of WC models by developing the first model that captures the function of each individual gene. We achieved the model through a combination of data integration, agent-based modeling, model composition, multi-algorithmic simulation, surrogate modeling, and unit testing. We have also shown how WC models can be used to discover biology, design microorganisms, and reposition drugs. This lecture will introduce the goals of WC modeling, the start-of-the-art of WC modeling, and model composition.