Modeling Approaches in Systems Biology, Including Silicon Cell Models

Alexey N. Kolodkin*, Fred C. Boogerd, Frank J. Bruggeman, Hans V. Westerhoff

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

7 Citations (Scopus)


To certain extent, biology is about explaining properties of living organisms in terms of interactions between particles of inorganic matter-macromolecules. Many properties of living organisms are usually strongly emergent; they cannot be deduced directly from the knowledge of macromolecules when these macromolecules are considered in isolation. Systems biology is about how to describe properties of these macromolecules as components of an entire system (how macromolecules interact with each other, how they are related in terms of concentrations and so on) in terms of mathematical equations. Solving these equations allows reconstructing strong emergence in silico. The chapter presents different approaches (top-down, bottom-up, middle-out) to reconstruct strong emergence in a computer model. The chapter discusses what a silicon cell model is and how computer modeling can be useful in the perspective of further development of livestock sciences.

Original languageEnglish
Title of host publicationSystems Biology and Livestock Science
Number of pages21
ISBN (Print)9780813811741
Publication statusPublished - 10 Oct 2011
Externally publishedYes


  • Bottom-up
  • Emergence
  • Middle-out
  • Silicon cell model
  • Systems biology
  • Top-down


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