Control running MATLAB application via a web page

I have a MATLAB program that runs for several hours controlling a piece of hardware and acquiring data. I monitor the output of the process by plotting graphs periodically and sending the images to the web. However, I sometimes would like to remotely tweak the data acquisition parameters (e.g. I've already gone home and noticed something isn't quite right). I currently do this by making an RDP connection to the Windows machine on which MATLAB is running and changing settings in a MATLAB GUI. However, RDP seems flaky and sometimes the machine reboots after I disconnect.

Ideally I would like to have a web interface which reports the current acquisition parameters and allows me to change these. I haven't thought of a good way of doing this yet. Has anyone done anything like this and has wisdom to share?