Systems Biology: Simulation of Dynamic Network States

Master the process of building MASS models with real examples and hands-on practice.

Large omics data sets are difficult to interpret and use, but this practical book teaches how to build complex dynamical models of biochemical networks and simulate their responses. All examples in the text are available in MATLAB® and Mathematica® workbooks, allowing easy hands-on practice.Biophysical models have been used in biology for decades, but they have been limited in scope and size. In this book, Bernhard Ø. Palsson shows how network reconstructions that are based on genomic and bibliomic data, and take the form of established stoichiometric matrices, can be converted into dynamic models using metabolomic and fluxomic data. The Mass Action Stoichiometric Simulation (MASS) procedure can be used for any cellular process for which data is available and allows a scalable step-by-step approach to the practical construction of network models. Specifically, it can treat integrated processes that need explicit accounting of small molecules and protein, which allows simulation at the molecular level. The material has been class-tested by the author at both the undergraduate and graduate level. All computations in the text are available online in MATLAB® and Mathematica® workbooks, allowing hands-on practice with the material.