Action-based analysis of discrete regulatory networks with short-term stimuli

Authors:
Christian Krause;Carola Krause;Erik P. de Vink
Affiliations:
Software Engineering, CWI Amsterdam;Leiden University Medical Center;Formal Methods, TU Eindhoven
Venue:
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
Year:
2010

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Abstract

To incorporate instant effects and different timescales within a single biological system, an extension of discrete regulatory networks with short-term stimuli is proposed. By maintaining a vector of recent changes, activities initiated by a steep increase or decrease can be captured in a qualitative setting. In order to compensate for the blow-up due to enhanced states, we focus on observable behavior. Identification of bisimilar states yields a compact system representation truthfully expressing the information relevant for deciding logical properties. The approach is implemented by means of a front-end to the mCRL2 tool set and illustrated for the switching of bacteriophage lambda and a bio-medical case study related to TGFβ driven fibrotic conditions.