I use bash scripting
stty -F /dev/ttyUSB0 cs8 115200 ignbrk -brkint -icrnl -imaxbel -opost -onlcr -isig -icanon -iexten -echo -echoe -echok -echoctl -echoke noflsh -ixon -crtscts -clocal
cat /dev/ttyUSB0|head -n 6|tail -n 3 >> /root/arduino #
The above sets ttyUSB0 to 115200 baud and reads the last 3 lines of 6 lines read into a file 'arduino' in roots home folder.
I have the arduino sending data out in space delimited lines of text in groups of 3 lines continuously. It reads 6 and takes the last 3 in case it joins the conversation part way through and corrupts the first line.
I send single character commands back to the arduino
echo 'Z' > /dev/ttyUSB0
If it resets the arduino each time (it may or may not depending on your computer) stick something like a 1 - 10uF capacitor across gnd and the reset pin to 'swallow' the DTR auto reset pulse.
I have it all running through cron every minute to produce :http://pluggy.is-a-geek.com/