Jeff,
There's a couple of ways to do this.
The way I've personally used most successfully is to use the System.Diagnostics.Process object. If it works, it tends to be more readable and accessible than directly making system calls.
proc = System.Diagnostics.Process;
proc.StartInfo.FileName = fullfile(exePath,exeName);
proc.StartInfo.Arguments = num2str(Port);
proc.Start(); % Start the process
To interface with the process, you can do a couple of different things:
1) My processes tend to be able to open TCP or UDP ports that I can communicate over, which is why my example passes a 'Port' argument into the process.
2) Alternatively you can use the process.standardinput streamwriter object if your proccess supports it.
https://msdn.microsoft.com/en-us/library/system.diagnostics.process.standardinput%28v=vs.110%29.aspx
3) The most work is to use robo calls - I haven't actually done this, but it looks like it may be feasible.
