Affiliations: [a] Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correnstrasse 3, 06466 Stadt Seeland, OT Gatersleben, Germany. maryann.blaetke@ovgu.de | [b] Chair of Data Structures and Software Dependability, Brandenburg University of Technology Cottbus-Senftenberg, Postbox 10 13 44, D-03013 Cottbus, Germany
Correspondence:
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Address for correspondence (present adress): Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correnstrasse 3, 06466 Stadt Seeland, OT Gatersleben, Germany; Also affiliated at: Department of Regulatory Biology, Otto-von-Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
Abstract: 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.
Keywords: modular model composition, spatial modelling, multiscale biomodel-engineering, coloured Petri nets
