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In silico investigations by simulating dynamical models of biochemical processes play an important role in systems biology. If the parameters of a model are unknown, results from simulation studies can be misleading. Such a scenario can be avoided by estimating the parameters before analysing the system. Almost all approaches for estimating parameters in ordinary differential equations have either a small convergence region or suffer from an immense computational cost. The method of multiple shooting can be situated in between of these extremes. In spite of its good convergence and stability properties, the literature regarding the practical implementation and providing some theoretical background is rarely available. All necessary information for a successful implementation is supplied here and the basic facts of the involved numerics are discussed. To show the performance of the method, two illustrative examples are discussed.