Constraint-Based Modeling in Systems Biology

1 pages•Published: May 15, 2012

Abstract

The idea of constraint-based modeling in systems biology is to describe a biological system by a set of constraints, i.e., by pieces of partial information about its structure and dynamics. Using constraint-based reasoning one may then draw conclusions about the possible system behaviors.

In this talk, we will focus on constraint-based modeling techniques for regulatory networks starting from the discrete logical formalism of René Thomas. In this framework, logic and constraints arise at two different levels. On the one hand, Boolean or multi-valued logic formulae provide a natural way to represent the structure of a regulatory network, which is given by positive and negative interactions (i.e., activation and inhibition) between the network components. On the other hand, temporal logic formulae (e.g. CTL) may be used to reason about the dynamics of the system, represented by a state transition graph or Kripke model.

In: Agostino Dovier, Alessandro Dal Palù and Sebastian Will (editors). WCB10. Workshop on Constraint Based Methods for Bioinformatics, vol 4, pages 1.

Links:	https://easychair.org/publications/paper/47rd
	https://doi.org/10.29007/8w4w

BibTeX entry

@inproceedings{WCB10:Constraint_Based_Modeling_Systems,
  author    = {Alexander Bockmayr},
  title     = {Constraint-Based Modeling in Systems Biology},
  booktitle = {WCB10. Workshop on Constraint Based Methods for Bioinformatics},
  editor    = {Agostino Dovier and Alessandro Dal Palù and Sebastian Will},
  series    = {EPiC Series in Computing},
  volume    = {4},
  publisher = {EasyChair},
  bibsource = {EasyChair, https://easychair.org},
  issn      = {2398-7340},
  url       = {/publications/paper/47rd},
  doi       = {10.29007/8w4w},
  pages     = {1},
  year      = {2012}}

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