... of concepts and approaches, with an emphasis on their possible applications. It presents key concepts and their theoretical background, including the concepts of robustness and modularity and their exploitation to study biological systems; the best-known modeling approaches, and their advantages...

...This chapter describes the importance of developmental systems to evolutionary variation and examines some general properties of biological systems that deconstrain phenotypic change. It argues that physiological variation, particularly the variation used in embryonic development, is an important...

...This chapter discusses some of the reasons for seeking to model complex cellular biological systems. It begins by presenting a philosophical overview and historical context. It then considers the purposes and implications of modeling; the different kinds of models; and sensitivity analysis...

... highly optimized tolerance HOT elementary flux modes EFMs metabolic fluxes flux analysis circadian oscillator parameter identification biological systems cellular complexity robustness central metabolism circadian clocks modeling The daunting complexity of cellular systems appears as a major...

...The complexity of biological systems requires unifying, simplifying concepts that might allow a predictive understanding of their functioning. Suggestions for such concepts include “modularity” along with robustness, discussed in Chapter 2. This chapter considers the existence of modules in biology...

...This chapter presents theoretical approaches for describing the dynamics of biological systems. The first part discusses continuum descriptions in terms of partial differential equations. Such a description is appropriate if one is interested in the dynamics on scales that are large compared...

... and that it is necessary to wait for a general theory of biology before a proper definition of life can be successfully articulated; however, the work of synthesis needed to generate and defend such a definition could actually help form the basis for a general theory of biological systems. The chapter elaborates...

...This chapter discusses the dynamical hierarchies in biological systems and molecular systems as well as higher-order dynamical hierarchies. In biological systems, hierarchies with multiple functionalities at different scales can be found everywhere. On the molecular level, novel functionalities can...

...This chapter studies a number of important aspects related to the plasticity and complexity of biological systems and their links. The relationship between the topological organization and dynamics of chromatin and chromosome, the regulatory proteins networks, and the mechanisms of genetic...

... properties differential equations Boolean networks graphs two-gene network biological systems There is a growing demand for methods that can make predictions of qualitative properties of the dynamics of molecular interaction networks, that is, properties that are invariant for a range of reaction...