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Stepwise Construction of a Metabolic Network in Event-B: The Heat Shock Response

Usman Sanwal, Luigia Petre, Ion Petre, Stepwise Construction of a Metabolic Network in Event-B: The Heat Shock Response. Computers in Biology and Medicine (91), 1–12, 2017.

http://dx.doi.org/10.1016/j.compbiomed.2017.09.021

Abstract:

There is a high interest in constructing large, detailed computational models for biological processes. This is often
done by putting together existing submodels and adding to them extra details/knowledge. The result of such
approaches is usually a model that can only answer questions on a very specific level of detail, and thus, ultimately,
is of limited use. We focus instead on an approach to systematically add details to a model, with formal
verification of its consistency at each step. In this way, one obtains a set of reusable models, at different levels of
abstraction, to be used for different purposes depending on the question to address. We demonstrate this approach
using Event-B, a computational framework introduced to develop formal specifications of distributed software
systems. We first describe how to model generic metabolic networks in Event-B. Then, we apply this method for
modeling the biological heat shock response in eukaryotic cells, using Event-B refinement techniques. The
advantage of using Event-B consists in having refinement as an intrinsic feature; this provides as a final result not
only a correct model, but a chain of models automatically linked by refinement, each of which is provably correct
and reusable. This is a proof-of-concept that refinement in Event-B is suitable for biomodeling, serving for
mastering biological complexity.

BibTeX entry:

@ARTICLE{jSaPePe17a,
  title = {Stepwise Construction of a Metabolic Network in Event-B: The Heat Shock Response},
  author = {Sanwal, Usman and Petre, Luigia and Petre, Ion},
  journal = {Computers in Biology and Medicine},
  number = {91},
  publisher = {Elsevier},
  pages = {1–12},
  year = {2017},
  ISSN = {0010-4825},
}

Belongs to TUCS Research Unit(s): Distributed Systems Laboratory (DS Lab), Computational Biomodeling Laboratory (Combio Lab)

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