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PICKLE can be queried and downloaded at http//www.pickle.gr. Supplementary data are available at Bioinformatics online. Supplementary data are available at Bioinformatics online. Cells are complex systems composed of hundreds of genes whose products interact to produce elaborated behaviors. To control such behaviors, cells rely on transcription factors to regulate gene expression, and gene regulatory networks (GRNs) are employed to describe and understand such behavior. However, GRNs are static models, and dynamic models are difficult to