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BioModelKit : Spatial Modelling of Complex Multiscale Molecular Biosystems Based on Modular Models

Blätke M.-A., Rohr C.

Fundamenta Informaticae

2018

Vol. 160, nr 1/2

221--254

Systems and synthetic biology require multiscale biomodel engineering approaches to integrate diverse spatial and temporal scales which will help to better understand and describe the various interactions in biological systems. Our BioModelKit framework for modular biomodel engineering allows composing multiscale models from a set of modules, each describing an individual biomolecular component in the form of a Petri net. In this framework, we now propose a feature for spatial modelling of molecular biosystems. The spatial model represents the coordinates and movement of individual biomolecular components on a defined grid. Here, the distance between components constrains their ability to interact with each other. We use coloured Petri nets to scale the spatial model, such that each molecular component can exist in an arbitrary number of instances. The grid can encode various regular and irregular structures according to the cellular arrangement and geometry. Furthermore, the grid can be divided into compartments to represent the compartmentalisation of the cell.