How fit a parameterised ode solution to experimental data

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I have a model, a system of Odes, defined by a set of parameters. I also have a number of raw experimental data sets. I want to find an optimal parameterisation, what is a method of doing so?
Does there exist functionality in matlab to score the fit of one data set to another? If so I can easily write an optimisation algorithm using fmincon.
Any help is greatly appreciated as I have not attempted something like this before.

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