SQUAD simulation results analysis using the SQUADD package

Logical modeling is increasingly popular method in system biology to explain and predict the behavior of a complex process (differentiation, cell growth, division etc. . . ) through their regulatory and signalling mechanisms. The SQUAD software (Standardized Qualitative Dynamical Systems) is dedicated to the analysis of Boolean logical models [1]. It was the first tool to combine the traditional Boolean approach and a continuous system. This novel feature permits the dynamical analysis of regulatory network in the absence of kinetic data [5], [4], [1]. In order to improve this approach, we provide the R package SQUADD, the SQUAD add-on. This extension permits: (i) to simplify the visualization of the initial SQUAD simulation output, (ii) to generate qualitative predictions of the component change between two conditions and (iii) to assess the coherence of a network model using PCA analysis.