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Syphonstat

Syphoning Turbidostat

The syphoning turbidostat is a simpler device than the Flexostat but uses many of the same parts. Infact the only new part necessary is the controller board (design files coming soon).

Quick links

design files: coming soon
Software: Repository download

Hookup guide

Schematic diagram of Syphonstat hookup

Figure showing hookup for laser(left header) and two-wire fan(right header). Note polarity.

Quickstart

1. Assemble closed system as shown in the hookup guide.
   1. If your media is autoclavable, add it now and make sure to clamp off all tubes going into the media bottle (loosen the lid/stopper to allow gas to vent)
2. Autoclave the closed system (Be sure to foil over any open ends including the PTFE filters)
3. Add media using sterile technique if not autoclavable.
4. Insert culture tube into culture chamber and place media bottle 1-3 feet above the culture tube.
5. Insert media line into pinch valve and unclamp media and air lines
6. Attach air line to media bottle
7. Check for pinch valve leaks
   1. If the media is passing through the valve check that the tube is in the normally closed (top) side and that you're tube is not undersized (very common). If you have undersized tube you can use a few layers of lab tape to make the valve smaller.
8. Press the override button on top of the pinch valve (or temporarily remove the tube from the valve) until the culture tube fills with media up to the effluent port.
9. Attach air line to culture chamber
10. On the PC remove any old log and dat files
11. Attach Power to the syphonstat controller board
12. If inoculating dense or a high volume of cells
    1. Start the software and wait at least 1 minute for the system to blank
    2. Innoculate by piercing the stopper with a syringe loaded with inoculum
13. If inoculating with few cells (OD~=0 when diluted to 15ml)
    1. Innoculate by piercing the stopper with a syringe loaded with inoculum
    2. Start the software and wait at least 1 minute for the system to blank

Software

The first time you run the software make sure you have python 2.7 or greater but not 3.x, the newest version of pySerial and the FTDI VCP serial drivers installed (newer versions of macOS and most distributions of linux should already have these drivers installed).

The software is currently a very simple command-line python script. To run the script open a command window in the syphonstat "python" directory and run 'python main.py'. Note on some systems (macOS and Linux) it may only be necissisary to type main.py but due to an issue with how windows deals with command line arguments the preferred way to invoke the program is 'python main.py'.

    Usage: main.py [options]
    Options: 
     -?, --help           Prints this message and exits.
     -t, --test           Test mode: displays sensor data as (tx,rx) and exits
         --port=PORT      Sets serial port to PORT.  For windows this should be in 
                          the form COMnnn eg COM1 or COM123.  For nix/MacOS use the
                          path to the serial device eg /dev/cu.usbserial
         --setpoint=f.ff  Sets the OD set point to f.ff OD units.  eg 0.40
         --logfile=of.dat Sets the file used to wirte out log data.

    Example: 
      Read sensor data to verify the device is working on COM5
    python main.py -t --port=COM5

      Run syphoning turbidostat on COM32 at 0.7 OD and write logs to history.dat
    python main.py --port=COM32 --setpoint=0.7 --logfile=history.dat