Hello, Before you open the serial device you should create a log file:
logFile = fopen(logFileName, 'wt');
The command to read from a serial device is:
serial_string = fscanf(SerialObj);
date_string = datestr(now);
fprintf(logFile,[date_string ' - ' serial_string]);
If you want to read the data each 3 minutes I would recommend you to use a timer ( http://www.mathworks.com/help/techdoc/ref/timer.html )
Hope it helps.