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I can give you a few tips
open_system('ModelName'); % opens a simulink model in the current directory
set_param('ModelName/Manual Switch','sw','1'); % closes a switch on you simulink model
set_param('ModelName/Gain','Gain', NewGain); % changes the Gain of a Gain block
Tsim = str2double(get(handles.edit1, 'String')); % get a value from a GUI textbox
sim('ModelName',[0 Tsim]); % Start the simulation of your model until Tsim (end time)
If you want to get data from your model to your GUI, for example you want to do a graph you can add a To Workspace simulink block connected to what you want to measure and also one To Workspace having for input the Clock (time), change its properties to some variable name like Value and plot it on a GUI axe like this:
axes(handles.axes1); % select on wich axe you want the graph
plot(time,Value); % do the graph
Hope this can help you but I don't have experience with data aquisition cards, sorry
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