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MOTIVATION To understand the behaviour of complex biological regulatory networks, a proper integration of molecular data into a full-fledge formal dynamical model is ultimately required. As most available data on regulatory interactions are qualitative, logical modelling offers an interesting framework to delineate the main dynamical properties of the(More)
Systems biologists are facing the difficult challenge of modelling and analysing regulatory networks encompassing numerous and diverse components and interactions. Furthermore, available data sets are often qualitative, which complicates the definition of truly quantitative models. In order to build comprehensive and predictive models, there is clearly a(More)
Many important problems in cell biology require the consideration of dense nonlinear interactions between functional modules. The requirement of computer simulation for the understanding of cellular processes is now widely accepted, and a variety of modelling frameworks have been designed to meet this need. Here, we present a novel public release of the(More)
The budding yeast cell cycle core engine has been modelled in great detail, most notably by the groups of Béla Novak and John Tyson, using a differential formalism. Several models focusing on different regulatory modules have been developed. In this respect, the use of a logical formalism facilitates the development of more integrated models, through the(More)
The Drosophila eggshell constitutes a remarkable system for the study of epithelial patterning, both experimentally and through computational modeling. Dorsal eggshell appendages arise from specific regions in the anterior follicular epithelium that covers the oocyte: two groups of cells expressing broad (roof cells) bordered by rhomboid expressing cells(More)
MOTIVATION Understanding the temporal behaviour of biological regulatory networks requires the integration of molecular information into a formal model. However, the analysis of model dynamics faces a combinatorial explosion as the number of regulatory components and interactions increases. RESULTS We use model-checking techniques to verify sophisticated(More)
The daily rhythm can influence the proliferation rate of many cell types [1]. In the mammalian system the transcription of the cell cycle regulatory protein Wee1 is controlled by the circadian clock [2]. In [3], Zámborszky et al. present a computational model of the cell cycle and circadian rhythm coupling, showing that the coupling can lead to multimodal(More)
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