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

• Autorzy: Blätke M.-A. , Rohr C.

Identyfikatory

DOI

10.3233/FI-2018-1682

• Języki publikacji: EN

Abstrakty

EN

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.

Słowa kluczowe

EN

modular model composition; spatial modelling; multiscale biomodel-engineering; coloured Petri nets

• Wydawca: IOS Press
• Czasopismo: Fundamenta Informaticae
• Rocznik: 2018
• Tom: Vol. 160, nr 1/2
• Strony: 221--254
• Opis fizyczny: Bibliogr. 29 poz., rys., tab.

Twórcy

autor

Blätke M.-A.

• Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correnstrasse 3, 06466 Stadt Seeland, OT Gatersleben, Germany

autor

Rohr C.

• Chair of Data Structures and Software Dependability, Brandenburg University of Technology Cottbus-Senftenberg, Postbox 10 13 44, D-03013 Cottbus, Germany

Bibliografia

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Uwagi

Opracowanie rekordu w ramach umowy 509/P-DUN/2018 ze środków MNiSW przeznaczonych na działalność upowszechniającą naukę (2018).