The markup is the model: reasoning about systems biology models in the Semantic Web era

J Theor Biol. 2008 Jun 7;252(3):538-43. doi: 10.1016/j.jtbi.2007.10.023. Epub 2007 Dec 3.


Metabolic control analysis, co-invented by Reinhart Heinrich, is a formalism for the analysis of biochemical networks, and is a highly important intellectual forerunner of modern systems biology. Exchanging ideas and exchanging models are part of the international activities of science and scientists, and the Systems Biology Markup Language (SBML) allows one to perform the latter with great facility. Encoding such models in SBML allows their distributed analysis using loosely coupled workflows, and with the advent of the Internet the various software modules that one might use to analyze biochemical models can reside on entirely different computers and even on different continents. Optimization is at the core of many scientific and biotechnological activities, and Reinhart made many major contributions in this area, stimulating our own activities in the use of the methods of evolutionary computing for optimization.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Algorithms
  • Animals
  • Databases, Factual
  • Internet
  • Metabolic Networks and Pathways / physiology*
  • Models, Biological*
  • Programming Languages
  • Software
  • Systems Biology / methods*