SO this is our first time using Simulink or any programming application, and we've hit a road block. We can't move the program into the controller or the brain. We've looked at the instructions and some tutorials but when we try to use it the most we get are quick power surges. Simulations run with no errors, but nothing else works. If anyone can help we would much appreciate it! Thanks
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Since "following the instructions" is the usual advice, its hard to say what might be the problem based on your description.
I don't think Simulink needs to program the joystick ("We can't move the program into the controller ").
Regarding "brain",  there were previous years BEST controllers called "brain", but we currently use the Vex controller called "Cortex", so that would be better terminology to use.
   "When we try to use it, the most we get are quick power surges"
Your Hypothesis: H1; program not getting loaded.
Alternate Hypothesis: H2 : your program is loaded, but doesn't do what you expected.
A test for H2 would be to use a "known good" code example. 

Can you explain in more detail "quick power surges"?

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In addition to jgraber's question, could you also let us know how are you 'downloading' the Simulink program to the VEX Cortex? Could you add a screenshot of the Simulink model that you are using for this test? 

It might be a good idea to watch these free training webinars to completely understand the workflow for Simulink beforehand. The second one goes over in detail about downloading to VEX Cortex:


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Use the orange USB cable to download the program from computer to the cortex. Next connect the cable from the cortex to the controller. Turn the cortex on first then turn the controller on.
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We had to call the Vex site and this is what they told us to do.  Download firmware and load default code. You also have to make sure the motor plugs into part 29 and then part 29 connect to cortex.. 
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Updating the VEX firmware as suggested before might be a good option. You would have to update the firmware on both the Cortex and the controller. Look for VEXNet Firmware Upgrade Utility (Zip) on this page:
There is a PDF manual with instructions inside the Zip-file. 

The part 29 that jmcgillivray mentions are the motor controller cables that should have been provided to you in the kit. More info on them:


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