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J Integr Bioinform. 2018 Sep 6;15(3). pii: /j/jib.2018.15.issue-3/jib-2018-0021/jib-2018-0021.xml. doi: 10.1515/jib-2018-0021.

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

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Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Corrensstrasse 3, 06466 Seeland OT Gatersleben, Germany.


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 (, 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.


Petri nets; model composition; model database; model mutation; spatiotemporal modelling

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