ABSTRACT
The idea to separate the total functionality of the cell into smaller pieces that could be modeled individually and then integrated was a critical aspect of our future strategy for modeling entire cells. The development of regulatory flux balance analysis (rFBA) also turned out to be a major step toward building whole-cell models. Like rFBA, whole-cell models bring together multiple modeling approaches into one integrated simulation; like rFBA and dynamic FBA, the process of whole-cell modeling resembles a numerical integrator. The whole-cell model has been incredibly exciting for lab at Stanford University. The simulations compare well with many different types of data. Models of more complex cells will need to consider issues such as detailed transcriptional regulation, compartmentalization, and detailed spatial modeling using ODEs. Unexpected hurdles will add even more spice to the development of whole-cell models, which is currently a very new field of research.
