How to train a Neural Network which is placed in a simulink block diagram as a controller through script files?

I've placed an initial Neural Network in my Simulink using gensim command. Now it's the time for training the network. On the other hand I've written my training algorithm code in the editor. On the training loop I have to call simulink system using sim command, process data and then update the weights and biases and go on. One way to do this is using set_param command to change the weights. But I need to write my algorithm adaptive to any network structure, I talk about number of hidden layers and neurons, without any need to change the training code. Any one has any idea about doing that?

I use Matlab R2012b engine.