Qualitative, Semi-quantitative, and Quantitative Simulation of the Osmoregulation System in Yeast

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Abstract

In this paper we demonstrate how Morven, a computational framework which can perform qualitative, semi-quantitative, and quantitative simulation of dynamical systems using the same model formalism, is applied to study the osmotic stress response pathway in yeast. First the Morven framework itself is briefly introduced in terms of the model formalism employed and output format. We then built a qualitative model for the biophysical process of the osmoregulation in yeast, and a global qualitative-level picture was obtained through qualitative simulation of this model. Furthermore, we constructed a Morven model based on existing quantitative model of the osmoregulation system. This model was then simulated qualitatively, semi-quantitatively, and quantitatively. The obtained simulation results are presented with an analysis. Finally the future development of the Morven framework for modelling the dynamic biological systems is discussed.
Original languageEnglish
Pages (from-to)40-50
Number of pages11
JournalBioSystems
Volume131
Early online date9 Apr 2015
DOIs
Publication statusPublished - May 2015

Fingerprint

Osmoregulation
Yeast
Yeasts
Biophysical Phenomena
Simulation
Osmotic Stress
Model
Qualitative Simulation
Biological Systems
Biological systems
Dynamic Systems
Pathway
Dynamical system
Dynamical systems
Model-based
Output
Modeling
Demonstrate
Framework

Keywords

  • osmotic stress response
  • Semi-quantitative simulation
  • qualitative simulation

Cite this

Qualitative, Semi-quantitative, and Quantitative Simulation of the Osmoregulation System in Yeast. / Pang, Wei; Coghill, George M.

In: BioSystems, Vol. 131, 05.2015, p. 40-50.

Research output: Contribution to journalArticle

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AB - In this paper we demonstrate how Morven, a computational framework which can perform qualitative, semi-quantitative, and quantitative simulation of dynamical systems using the same model formalism, is applied to study the osmotic stress response pathway in yeast. First the Morven framework itself is briefly introduced in terms of the model formalism employed and output format. We then built a qualitative model for the biophysical process of the osmoregulation in yeast, and a global qualitative-level picture was obtained through qualitative simulation of this model. Furthermore, we constructed a Morven model based on existing quantitative model of the osmoregulation system. This model was then simulated qualitatively, semi-quantitatively, and quantitatively. The obtained simulation results are presented with an analysis. Finally the future development of the Morven framework for modelling the dynamic biological systems is discussed.

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