• Pump 1: Used to pump out medium from the reactor bottle into the OD chamber and finally to the waste bottle
• Pump 2: Used to dilute the reactor medium with fresh sterile medium if needed.
• Pump 3: Used to pump out reactor medium through the heating block and the fluorescence chamber into another waste bottle.
• Arduino 1: Arduino controlling the H-Bridge module that had the peristaltic pumps attached.
• Arduino 2: Arduino running the OD-measuring code, sending GPIO signals to Arduino 1 if necessary.

               Arduino 2 was used to run the "Aachen final.ino", an Arduino code used by the former igem team Aachen to measure the optical
               density of a medium with the "TSL 235R-sensor". Before use, the system had to be calibrated with samples
               of known OD (measured with a laboratory OD-device). The output value was transformed into real OD-values
               for better control of the experiment. Then a "switch case" code was written that used this output value to
               decide whether fresh medium was needed to dilute the reactor medium or if a defined pause was needed for
               the next measuring cycle. The Arduino 2 communicated with Arduino 1 via GPIO signals.

               For a measuring cycle the coding on the Arduino 1 was designed as follows: After 20 minutes had passed, a small amount of
               medium was pumped out of the reactor and through the OD-chamber from below. Then a 5 second delay was used
               for any bubbles inside the chamber to dissociate. A delay ensured Arduino 2 to measure the optical density
               in the meantime. Then the code was waiting for GPIO signals of Arduino 2 that triggered the pump 2 if necessary.
               Our experiments showed that the optimal optical density for proper fluorescence signals was at OD = 0.3.
               The OD-maintenance system was set to this value and was able to keep the OD at ~ 0.3 over a long period of
               time (or until there was no fresh medium left)  .Whenever an OD > 0.3 was reached, approx. 5 mL of fresh
               sterile medium was pumped into the reactor bottle.

               One problem that came up was that the liquid level inside the reactor bottle had to stay the same over longer periods of
               time. Since liquid was pumped out of the reactor bottle every 20 minutes for OD measurements and for fluorescence
               measurements by the other pump, liquid levels dropped relatively fast and the reactor bottle was empty pretty
               quick in first trials. The solution was to measure the volumes transferred by the peristaltic pumps for specific
               running times. Then it was possible to adjust the liquid level inside the reactor bottle by changing the
               Arduino code since the guesstimate volumes were known. Every pumped out volume of reactor medium was replaced
               with the same amount of fresh sterile medium after this adjustment.