Systems Biology: Simulation of Dynamic Network States

Systems Biology: Simulation of Dynamic Network States

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Biophysical models have been used in biology for decades, but they have been limited in scope and size. In this book, Bernhard A˜. 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 MATHEMATICAAr workbooks, allowing hands-on practice with the material.Neema Jamshidi has been an MD/PhD student in my lab over the past 6 or 7 years. He has been a fantastic colleague and friend. He educated me about the use of Mathematica and tirelessly answered my repeated and often naive questions.

Title:Systems Biology: Simulation of Dynamic Network States
Author:Bernhard Ø. Palsson
Publisher:Cambridge University Press - 2011-05-26


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