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Representing and Analyzing Biochemical Networks Using BioMaze

  • Yves Deville
  • Christian Lemer
  • Shoshana Wodak

Abstract

Systems biology aims at understanding the holistic behavior of biological systems. A very important step toward this goal is to develop a theoretical framework in which we can embed the detailed knowledge that biologists are accumulating at increasing speed, which will then allow us to compute the outcomes of the complex interplay between the myriad interactions that take place in the system. This chapter deals with important basic aspects of this theoretical framework that lie on the divide between systems biology and bioinformatics. In the first part, it discusses the conceptual models used for representing detailed knowledge on various types of biochemical pathways and interactions. As much of this knowledge deals with the complex networks of functional and physical interactions between the different molecular players, the second part of this chapter reviews the conceptual models and methods used to analyze various properties of these networks.

Key Words

Biochemical networks network analysis metabolic pathways signal transduction artificial intelligence BioMaze 

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Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • Yves Deville
    • 1
  • Christian Lemer
    • 2
  • Shoshana Wodak
    • 3
  1. 1.Computing Science and Engineering DepartmentUniversité Catholique de LouvainLouvain-la-NeuveBelgium
  2. 2.Unité de Conformation des Macromolécules BiologiquesUniversité Libre de BruxellesBruxellesBelgium
  3. 3.Department of Biochemistry and Structural Biology, Department of Medical GeneticsUniversity of TorontoTorontoCanada

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