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Mathematical modeling of biological processes is a useful tool to draw conclusions that are contained in the data, but not directly reachable, as well as to make predictions and select the most efficient follow-up experiments. Here we outline a method to model systems of a few proteins that interact transcriptionally and/or posttranscriptionally, by representing the system as Ordinary Differential Equations and to study the model dynamics and stationary states. We exemplify this method by focusing on the regulation by the brassinosteroid (BR) signaling component BRASSINOSTEROID INSENSITIVE1 ETHYL METHYL SULFONATE SUPPRESSOR1 (BES1) of BRAVO, a quiescence-regulating transcription factor expressed in the quiescent cells of Arabidopsis thaliana roots. The method to extract the stationary states and the dynamics is provided as a Mathematica code and requires basic knowledge of the Mathematica software to be executed., D.F. and M.I. acknowledge support from the Ministerio de Economía y Competitividad (Spain) and FEDER (EU) through grant FIS2015-66503-C3-3-P and from the Generalitat de Catalunya through Grup de Recerca Consolidat 2014 SGR 878. AIC-D acknowledges financial support from the Spanish Ministry of Economy and Competitiveness, through the ‘Severo Ochoa Programme for Centres of Excellence in R&D’ 2016–2019 (SEV-2015-0533). AIC-D is a recipient of a BIO2013-43873 grant from the Spanish Ministry of Economy and Competitiveness and European Research Council, ERC Consolidator Grant (ERC-2015-CoG – 683163).