Inferring Biological Mechanisms by Data-Based Mathematical Modelling Compartment-Specific Gene Activation during Sporulation in Bacillus subtilis as a Test Case.pdfVIP

Hindawi Publishing Corporation Advances in Bioinformatics Volume 2011, Article ID 124062, 12 pages doi:10.1155/2011/124062 Review Article Inferring Biological Mechanisms by Data-Based Mathematical Modelling: Compartment-Specific Gene Activation during Sporulation in Bacillus subtilis as a Test Case Dagmar Iber Department for Biosystems Science and Engineering, Switzerland and Swiss Institute of Bioinformatics (SIB), ETH Zurich, Mattenstraße 26, Basel 4058, Switzerland Correspondence should be addressed to Dagmar Iber, dagmar.iber@bsse.ethz.ch Received 1 September 2011; Revised 12 October 2011; Accepted 3 November 2011 Academic Editor: Allegra Via Copyright © 2011 Dagmar Iber. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Biological functionality arises from the complex interactions of simple components. Emerging behaviour is difficult to recognize with verbal models alone, and mathematical approaches are important. Even few interacting components can give rise to a wide range of different responses, that is, sustained, transient, oscillatory, switch-like responses, depending on the values of the model parameters. A quantitative comparison of model predictions and experiments is therefore important to distinguish between competing hypotheses and to judge whether a certain regulatory behaviour is at all possible and plausible given the observed F type and strengths of interactions and the speed of reactions. Here I will review a detailed model for the transcription factor σ