Modelling Cell Cycle using Different Levels of Representation

TL;DR

This paper presents a formal methodology using Spatial CLS to model biological systems at multiple levels of representation, enabling detailed simulation and visualization of complex processes like the yeast cell cycle.

Contribution

It introduces a multi-level modeling approach combining biochemical dynamics and visual representations within a formal framework.

Findings

Successful modeling of the yeast cell cycle at different abstraction levels

Enhanced visualization capabilities for biological system simulation

Formal methodology facilitates comprehensive in silico experiments

Abstract

Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform computerised simulations of biological systems, which are called in silico experiments, to attain important insights and predictions about the system behaviour with a considerably lower cost. Computer visualisation is an important part of this approach, since it provides a realistic representation of the system behaviour. We define a formal methodology to model biological systems using different levels of representation: a purely formal representation, which we call molecular level, models the biochemical dynamics of the system; visualisation-oriented representations, which we call visual levels, provide views of the biological system at a higher level of organisation and are equipped with the necessary spatial information to generate the appropriate visualisation. We choose Spatial CLS, a formal language belonging to the class of Calculi of Looping Sequences, as the formalism for modelling all representation levels. We illustrate our approach using the budding yeast cell cycle as a case study.