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The main problems in modelling of any biological process are to take into account all the key parameters and to choose the tool to achieve the adequate model. Over recent years we have reported on several SEB Annual Main Meetings that mechanisms of the Arabidopsis root growth and development in the dark differ from those established for the light-grown plants. The importance of the darkness for the understanding root biology was also highlighted in several articles in top journals in biology by other researchers last year. The problem is that most of the detailed knowledge of many processes involved in root growth and development was achieved by studying light-grown Arabidopsis roots.