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.
Highlights
Quantitative modelling approaches have been widely used in the field of systems biology
The simulation results indicate that starting from the same qualitative status, the biophysical system may demonstrate different stress response behaviours, each of which corresponds to a path extracted from the envisionment graph
We first demonstrated that a Morven qualitative model can be built from scratch based on an initial understanding about the biophysical process of the osmoregulation system
Summary
Quantitative modelling approaches have been widely used in the field of systems biology They offer precise descriptions of the dynamics of biological systems, provide deeper understanding of the underlying mechanisms, and can predict possible behaviours of the system. As for the third issue, quantitative modellers tend to either assume precise measurements or estimate the initial conditions by statistical methods. Such assumptions and estimates may result in inaccurate predictions of the system, especially when the measurements are sparse and noisy. We present a solution to address the abovementioned issues, the Morven framework (Coghill, 1996; Bruce and Coghill, 2005) This solution covers a broad spectrum of levels of abstraction: quantitative, semi-quantitative, and qualitative.
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