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Constraint-based modeling of metabolomic systems

Part 3. Proteomics

3.8. Systems Biology

Specialist Review

  1. Daniel A. Beard1,
  2. Hong Qian2

Published Online: 15 APR 2005

DOI: 10.1002/047001153X.g308203

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Beard, D. A. and Qian, H. 2005. Constraint-based modeling of metabolomic systems. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 3:3.8:112.

Author Information

  1. 1

    Medical College of Wisconsin, Milwaukee, WI, USA

  2. 2

    University of Washington, Seattle, WA, USA

Publication History

  1. Published Online: 15 APR 2005


Constraint-based analysis of large-scale metabolic systems is the computational exploration of metabolic fluxes and concentrations constrained by the physical chemical laws of mass conservation and thermodynamics. This chapter reviews the mathematical formulation of the constraints on reaction fluxes and reactant concentrations that arise as a consequence of the stoichiometry of a specified network of biochemical reactions. Linear algebraic constraints arising from steady state mass balance form the basis of the related computational technologies metabolic flux analysis (MFA) and flux-balance analysis (FBA). Thermodynamic laws, while introducing inherent nonlinearities into the mathematical description of the feasible space, facilitate the introduction of reactant concentrations to the constraint-based framework. Together, the mass-balance and thermodynamic constraints form the basis of an approach to modeling and analysis of biochemical systems that is alternate and complementary to detailed chemical kinetics.


  • metabolic networks;
  • constraint-based modeling;
  • network thermodynamics;
  • computational modeling