Open AccessJournal Article
Using Hybrid concurrent constraint programming to model dynamic biological systems
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TL;DR: In this paper, the authors show that hybrid concurrent constraint programming (Hybrid cc) can be used naturally to model a variety of biological phenomena, such as reaching thresholds, kinetics, gene interaction or biological pathways.
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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 different parts of a biological system interact in order to perform complex biological functions. Computational models that help to analyze, explain or predict the behavior of biological systems play a crucial role in systems biology. The goal of this paper is to show that hybrid concurrent constraint programming [11] may be a promising alternative to existing modeling approaches in systems biology. Hybrid cc is a declarative compositional programming language with a well-defined semantics. It allows one to model and simulate the dynamics of hybrid systems, which exhibit both discrete and continuous change. We show that Hybrid cc can be used naturally to model a variety of biological phenomena, such as reaching thresholds, kinetics, gene interaction or biological pathways.
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Citations
BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge
TL;DR: BIOCHAM provides tools and languages for describing protein networks with a simple and straightforward syntax, and for integrating biological properties into the model, and it then becomes possible to analyze, query, verify and maintain the model with respect to those properties.
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Symbolic Model Checking of Biochemical Networks
Nathalie Chabrier,François Fages +1 more
- 24 Feb 2003
TL;DR: It is argued that symbolic model checking is feasible in systems biology and that it shows some advantages over simulation for querying and validating formal models of biological processes.
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An overview of data models for the analysis of biochemical pathways
TL;DR: The different types of data models found in the literature are classified using a unified framework to underline the strengths and weaknesses of the different approaches, as well as to highlight relevant future research directions.
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A rule-based model of barley morphogenesis, with special respect to shading and gibberellic acid signal transduction
Gerhard Buck-Sorlin,Reinhard Hemmerling,Ole Kniemeyer,Ole Kniemeyer,Benno Burema,Winfried Kurth +5 more
TL;DR: The RGG formalism is suitable for implementation of multi-scaled FSPM of plants interacting with their environment via hormonal control, however, their ensuing complexity requires careful design.
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