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  3. Systems Biology: Simulation of Dynamic Network States
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    • Publisher:
      Cambridge University Press
      Publication date:
      August 2012
      May 2011
      ISBN:
      9780511736179
      9781107001596
      DOI:
      https://doi.org/10.1017/CBO9780511736179
      Dimensions:
      (247 x 174 mm)
      Weight & Pages:
      0.8kg, 332 Pages
      Dimensions:
      Weight & Pages:
      • Subjects:
      Genomics, Bioinformatics and Systems Biology, Life Sciences, Engineering, Biomedical Engineering
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    Subjects:
    Genomics, Bioinformatics and Systems Biology, Life Sciences, Engineering, Biomedical Engineering
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    Book description

    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.

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