Systems Biology: Simulation of Dynamic Network States

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

Bernhard Ø. Palsson (Author)

9781107001596, Cambridge University Press

Hardback, published 26 May 2011

332 pages, 126 b/w illus.
25.4 x 18.2 x 2.5 cm, 0.8 kg

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.

Preface
1. Introduction
2. Basic concepts
Part I. Simulation of Dynamic States: 3. Dynamic simulation: the basic procedure
4. Chemical reactions
5. Enzyme kinetics
6. Open systems
Part II. Biological Characteristics: 7. Orders of magnitude
8. Stoichiometric structure
9. Regulation as elementary phenomena
Part III. Metabolism: 10. Glycolysis
11. Coupling pathways
12. Building networks
Part IV. Macromolecules: 13. Hemoglobin
14. Regulated enzymes
15. Epilogue
A. Nomenclature
B. Homework problems
References
Index.

Subject Areas: Data mining [UNF], Molecular biology [PSD], Mathematical modelling [PBWH]