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From quantitative SBML models to boolean networks

Athénaïs Vaginay 1, 2 Taha Boukhobza 1, 2 Malika Smaïl-Tabbone 2 
2 CAPSID - Computational Algorithms for Protein Structures and Interactions
Inria Nancy - Grand Est, LORIA - AIS - Department of Complex Systems, Artificial Intelligence & Robotics
Abstract : Modelling complex biological systems is necessary for their study and understanding. SBML is the standard format to represent models of biological systems. Most of the curated models available in the repository Biomodels are quantitative, but in some cases qualitative models-such as Boolean networks-would be better suited. This paper is the first to focus on the automatic transformation of quantitative SBML models to Boolean networks. We propose SBML2BN, a pipeline dedicated to this task. By running SBML2BN on more than 200 quantitative SBML models, we provide evidence that we can automatically construct Boolean networks which are compatible with the structure and the dynamics of a given quantitative SBML model.
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Submitted on : Wednesday, December 15, 2021 - 12:17:53 PM
Last modification on : Wednesday, March 23, 2022 - 3:40:45 AM
Long-term archiving on: : Wednesday, March 16, 2022 - 6:49:39 PM


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  • HAL Id : hal-03481396, version 1


Athénaïs Vaginay, Taha Boukhobza, Malika Smaïl-Tabbone. From quantitative SBML models to boolean networks. 10th International Conference on Complex Networks and their Applications, CNA 2021, Nov 2021, Madrid, Spain. ⟨hal-03481396⟩



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