BioModelKit – An Integrative Framework for Multi-Scale Biomodel-Engineering

Abstract

While high-throughput technology, advanced techniques in biochemistry and molecular biology have become increasingly powerful, the coherent interpretation of experimental results in an integrative context is still a challenge. BioModelKit (BMK) approaches this challenge by offering an integrative and versatile framework for biomodel-engineering based on a modular modelling concept with the purpose: (i) to represent knowledge about molecular mechanisms by consistent executable sub-models (modules) given as Petri nets equipped with defined interfaces facilitating their reuse and recombination; (ii) to compose complex and integrative models from an ad hoc chosen set of modules including different omic and abstraction levels with the option to integrate spatial aspects; (iii) to promote the construction of alternative models by either the exchange of competing module versions or the algorithmic mutation of the composed model; and (iv) to offer concepts for (omic) data integration and integration of existing resources, and thus facilitate their reuse. BMK is accessible through a public web interface (www.biomodelkit.org), where users can interact with the modules stored in a database, and make use of the model composition features. BMK facilitates and encourages multi-scale model-driven predictions and hypotheses supporting experimental research in a multilateral exchange.

Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems

“…Besides, Blätke et al [69, 70] briefly discussed the use of ColPNs to represent a 3 D lattice of space, which can be fitted with a topological 3 D model of an entire cell. In their approach, they simulate biochemical reactions in a reaction–diffusion system with the help of a localization component.…”