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Open Access Highly Accessed Research article

Model composition through model reduction: a combined model of CD95 and NF-κB signaling pathways

Elena Kutumova12*, Andrei Zinovyev345, Ruslan Sharipov16 and Fedor Kolpakov12

Author affiliations

1 Institute of Systems Biology, Ltd, 15 Detskiy proezd, Novosibirsk 630090 Russia

2 Design Technological Institute of Digital Techniques, The Siberian Branch of The Russian Academy of Sciences, 6 Acad. Rzhanov Str, Novosibirsk 630090 Russia

3 Institut Curie, 26 rue d’Ulm, F-75248 Paris, France

4 INSERM U900, Paris F-75248 France

5 Mines ParisTech, Fontainebleau F-77300 France

6 Institute of Cytology and Genetics, The Siberian Branch of The Russian Academy of Sciences, 10 Acad. Lavrentyev Ave, Novosibirsk 630090 Russia

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Citation and License

BMC Systems Biology 2013, 7:13  doi:10.1186/1752-0509-7-13

Published: 15 February 2013

Abstract

Background

Many mathematical models characterizing mechanisms of cell fate decisions have been constructed recently. Their further study may be impossible without development of methods of model composition, which is complicated by the fact that several models describing the same processes could use different reaction chains or incomparable sets of parameters. Detailed models not supported by sufficient volume of experimental data suffer from non-unique choice of parameter values, non-reproducible results, and difficulty of analysis. Thus, it is necessary to reduce existing models to identify key elements determining their dynamics, and it is also required to design the methods allowing us to combine them.

Results

Here we propose a new approach to model composition, based on reducing several models to the same level of complexity and subsequent combining them together. Firstly, we suggest a set of model reduction tools that can be systematically applied to a given model. Secondly, we suggest a notion of a minimal complexity model. This model is the simplest one that can be obtained from the original model using these tools and still able to approximate experimental data. Thirdly, we propose a strategy for composing the reduced models together. Connection with the detailed model is preserved, which can be advantageous in some applications. A toolbox for model reduction and composition has been implemented as part of the BioUML software and tested on the example of integrating two previously published models of the CD95 (APO-1/Fas) signaling pathways. We show that the reduced models lead to the same dynamical behavior of observable species and the same predictions as in the precursor models. The composite model is able to recapitulate several experimental datasets which were used by the authors of the original models to calibrate them separately, but also has new dynamical properties.

Conclusion

Model complexity should be comparable to the complexity of the data used to train the model. Systematic application of model reduction methods allows implementing this modeling principle and finding models of minimal complexity compatible with the data. Combining such models is much easier than of precursor models and leads to new model properties and predictions.