Hello Panagiota,
I'd recommend purging the tubes prior to calibration, and prior to each day's training.
If you are using 1/16" ID silicone tubing (e.g. the tubing I referenced), you can manually override the solenoid valve to open the tube. Gravity will flush out any air bubbles. I'd use a 60ml syringe if possible. After purging the tube, refill the syringe to the same fluid level you used when starting calibration.
If the positions of the syringe and the drink tube are fixed, you will not need to calibrate very frequently. You can use the 'Test Curve' button on the liquid calibration GUI to ensure that calibration is still within tolerance. I'd test calibration daily at first, and less frequently as warranted. In my own research, I found that recalibrating was typically only necessary every month or so with a fixed rig.
Of course if you replace the tubing or change the position of the syringe and/or the drink tube you'll need to calibrate immediately after those changes.
I'd recommend that the tubing between the syringe and mouse port be as short as is practical in your assay. Up to 1 meter is common. Keep in mind that fluid flow is governed by Poiseuille's Law, so resistance is proportional to the length of tubing. Higher resistance translates into a longer valve pulse, which is accounted for in the calibration process.
-Josh
