Modeling metabolic networks for mammalian cell systems: General considerations, modeling strategies, and available tools

Abstract

Over the past decades, the availability of large amounts of information regarding cellular processes and reaction rates, along with increasing knowledge about the complex mechanisms involved in these processes, has changed the way we approach the understanding of cellular processes. We can no longer rely only on our intuition for interpreting experimental data and evaluating new hypotheses, as the information to analyze is becoming increasingly complex. The paradigm for the analysis of cellular systems has shifted from a focus on individual processes to comprehensive global mathematical descriptions that consider the interactions of metabolic, genomic, and signaling networks. Analysis and simulations are used to test our knowledge by refuting or validating new hypotheses regarding a complex system, which can result in predictive capabilities that lead to better experimental design. Different types of models can be used for this purpose, depending on the type and amount of information available for the specific system. Stoichiometric models are based on the metabolic structure of the system and allow explorations of steady state distributions in the network. Detailed kinetic models provide a description of the dynamics of the system, they involve a large number of reactions with varied kinetic characteristics and require a large number of parameters. Models based on statistical information provide a description of the systemwithout information regarding structure and interactions of the networks involved. The development of detailed models for mammalian cellmetabolismhas only recently started to growmore strongly, due to the intrinsic complexities of mammalian systems, and the limited availability of experimental information and adequatemodeling tools. In thisworkwe reviewthe strategies, tools, current advances, and recent models of mammalian cells, focusing mainly on metabolism, but discussing themethodology applied to other types of networks aswell. © Springer-Verlag Berlin Heidelberg 2011.