Using Arduino through Matlab

Hey,
I've been trying to connect my arduino to matlab and run then run another arduino script. I'll just give you a list of what ive done.

  1. Upload adio.pde from ArduinoIO package.
  2. Connect to Matlab using h = arduino('COM3')
  3. Upload new arduino code.

The third step gives the following error:
Serial port 'COM3' already in use. Try quitting any programs that may be using it.

I realize that the problem is because I still have the arduino connected to Matlab. I'm wondering if there is anyway to keep that connection and still run new arduino code. I've used the same arduino on a linux computer at my school, and was able to use the code
h = arduinoIO([1 0 1]);

to connect.(however this was most likely written by my professor). Any suggestions?

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