## Using Hybrid Concurrent Constraint Programming to Model Dynamic Biological Systems (2002)

Venue: | 18th International Conference on Logic Programming |

Citations: | 28 - 0 self |

### BibTeX

@INPROCEEDINGS{Bockmayr02usinghybrid,

author = {Alexander Bockmayr and Arnaud Courtois},

title = {Using Hybrid Concurrent Constraint Programming to Model Dynamic Biological Systems},

booktitle = {18th International Conference on Logic Programming},

year = {2002},

pages = {85--99},

publisher = {Springer}

}

### OpenURL

### Abstract

Systems biology is a new area in biology that aims at achieving a systems-level understanding of biological systems. While current genome projects provide a huge amount of data on genes or proteins, lots of research is still necessary to understand how the dierent parts of a biological system interact in order to perform complex biological functions.

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Citation Context ... 2 Existing modeling approaches A variety of formalisms for modeling biological systems has been proposed in the literature. A detailed discussion goes far beyond the scope of this paper, we refer to =-=[6,-=- 3] for an overview. Following [9], we may distinguish three basic approaches discrete, continuous, stochastic, and various combinations between them. Discrete models are based on discrete variable... |

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Citation Context ..., to represent dierent levels of gene expression. Several authors have started to apply concepts and tools from formal verication to model biological systems, like Petri nets [18] or the -calculus [19=-=-=-]. Continuous models have been used in mathematical biology for a very long time [25]. They are based on dierential equations that typically model biochemical reactions. By making certain assumptions,... |

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Citation Context ... in which case further action is taken [20]. The original cc framework has been extended in various directions. In the context of this paper, we are interested in the following extensions: Timed cc [=-=-=-21] Timed Default cc [22] Hybrid cc [12, 11, 4] One major diculty in the original cc framework is that cc programs can detect only the presence of information, not its absence. To overcome this prob... |

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Citation Context ...number of projects like BioSpice, Cellerator, DBSolve, E-Cell, Gepasi, Jarnac, ProMot/DIVA, StochSim or Virtual Cell aim at modeling and simulating biological processes. The Systems Biology Workbench =-=[13-=-] is a software platform currently being developed in order to enable the dierent tools to interact with each other. From a programming language perspective, a fundamental question arises: what is the... |

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Citation Context ...ne presented in Sect. 4.2. Typical situations where probabilities are used in modeling include: Simplied representation of processes (e.g. simulating the pathway choice of -phages in a population [8]). Integration of stochastic noise in order to get more realistic models. Large-scale Monte Carlo simulations. 3 Hybrid concurrent constraint programming Constraint programming started inside logi... |

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Citation Context ...variety of formalisms for modeling biological systems has been proposed in the literature. A detailed discussion goes far beyond the scope of this paper, we refer to [6, 3] for an overview. Following =-=-=-[9], we may distinguish three basic approaches discrete, continuous, stochastic, and various combinations between them. Discrete models are based on discrete variables and discrete state changes. A... |

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Citation Context ...0]. The original cc framework has been extended in various directions. In the context of this paper, we are interested in the following extensions: Timed cc [21] Timed Default cc [22] Hybrid cc [12=-=, 11, 4-=-] One major diculty in the original cc framework is that cc programs can detect only the presence of information, not its absence. To overcome this problem, [21] proposed to add to the cc paradigm a s... |

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2 | A.: Modeling biological systems in hybrid concurrent constraint programming (Abstract
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Citation Context ...ical pathways have their natural counterpart in Hybrid cc. Sect. 5 summarizes the discussion and points out directions for further research. The results presented in this paper were rst announced in [=-=2]-=-, see also [5]. 2 Existing modeling approaches A variety of formalisms for modeling biological systems has been proposed in the literature. A detailed discussion goes far beyond the scope of this pape... |

1 |
Modlisation de systmes biologiques en programmation par contraintes. Rapport de DEA (in
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Citation Context ...have their natural counterpart in Hybrid cc. Sect. 5 summarizes the discussion and points out directions for further research. The results presented in this paper were rst announced in [2], see also [=-=5]-=-. 2 Existing modeling approaches A variety of formalisms for modeling biological systems has been proposed in the literature. A detailed discussion goes far beyond the scope of this paper, we refer to... |

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The origins of order. Oxford Univ
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Citation Context ...ntinuous, stochastic, and various combinations between them. Discrete models are based on discrete variables and discrete state changes. A classical example are Boolean networks for gene regulation [=-=15-=-]. For each gene, there is a Boolean variable indicating whether or not the gene is expressed in a given state. Boolean functions are then used to relate the variables belonging to dierent states. Qua... |