Modelling Cell Cycle using Different Levels of Representation

Thomas Anung Basuki
(International Institute of Software Technology, United Nations University)
Antonio Cerone
(International Institute of Software Technology, United Nations University)
Rafael V. Carvalho
(International Institute of Software Technology, United Nations University)

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.

In Gabriel Ciobanu: Proceedings Third Workshop on Membrane Computing and Biologically Inspired Process Calculi 2009 (MeCBIC 2009), Bologna, Italy, 5th September 2009, Electronic Proceedings in Theoretical Computer Science 11, pp. 51–69.
Published: 30th November 2009.

ArXived at: http://dx.doi.org/10.4204/EPTCS.11.4 bibtex PDF

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