The article deals with the problems of formal description of methods of organization of biomedical experiment. The need for a formal description of the experimental scheme is postulated. One of the ways of formal representation of the biomedical experiment based on the transition graph, which is one of the variants of the description of the finite state machine, is considered. The description revealed that the main characteristics of this representation are the correctness and adequacy of the representation in the form of a graph of transitions. The problem of description of nested sequences of actions corresponding to the beginning and end of the use of different components of the experiment is considered. An example of such use is the serial and parallel activation of experimental equipment. In this case, the correct sequences correspond to the implemented experiments, and the wrong ones correspond to the unrealizable ones. In this regard, there is a need to verify such feasibility. The necessity of checking the correctness of the graph as the main condition for the feasibility of the experiment is substantiated. One of the approaches to the analysis of the correctness of such a graph on the basis of matrix calculations is presented. The method of constructing the transition graph matrix is considered. The basic transformations necessary for checking the correctness of the transition graph of the biomedical experiment are given.