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Quantitative Model Refinement as a Solution to the Combinatorial Size Explosion of Biomodels

Elena Czeizler, Eugen Czeizler, Bogdan Iancu, Ion Petre, Quantitative Model Refinement as a Solution to the Combinatorial Size Explosion of Biomodels. Electronic Notes in Theoretical Computer Science 284, 35–53, 2012.

http://dx.doi.org/10.1016/j.entcs.2012.05.014

Abstract:

Building a large system through a systematic, step-by-step refinement of an initial abstract specification is a well established technique in software engineering, not yet much explored in systems biology. In the case of systems biology, one starts from an abstract, high-level model of a biological system and aims to add more and more details about its reactants and/or reactions, through a number of consecutive refinement steps. The refinement should be done in a quantitatively correct way, so that (some of) the numerical properties of the model (such as the experimental fit and validation) are preserved. In this study, we focus on the data-refinement mechanism where the aim is to increase the level of details of some of the reactants of a given model. That is, we analyse the case when a model is refined by substituting a given species by several types of subspecies. We show in this paper how the refined model can be systematically obtained from the original one. As a case study for this methodology we choose a recently introduced model for the eukaryotic heat shock response, Petre(2011:595- 612). We refine this model by including details about the acetylation of the heat shock factors and its influence on the heat shock response. The refined model has a significantly higher number of kinetic parameters and variables. However, we show that our methodology allows us to preserve the experimental fit/validation of the model with minimal computational effort.

BibTeX entry:

@ARTICLE{inpCzCzIaPe12b,
  title = {Quantitative Model Refinement as a Solution to the Combinatorial Size Explosion of Biomodels},
  author = {Czeizler, Elena and Czeizler, Eugen and Iancu, Bogdan and Petre, Ion},
  journal = {Electronic Notes in Theoretical Computer Science},
  volume = {284},
  publisher = {Elsevier},
  pages = {35–53},
  year = {2012},
  keywords = {Model refinement; quantitative analysis; heat shock response; acetylation},
}

Belongs to TUCS Research Unit(s): Computational Biomodeling Laboratory (Combio Lab)

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