Set-up worked – but a test run with just water won’t work

[NaomivdB]

Hi all,

Having set up the operating system and everything, I was hoping today to start a test run with just water being pumped in and out of the reactor. Using the web user interface, I set everything to 0 except for volume, temperature and pump rate ofcourse (in and out both at 1, although I tried different orders of magnitude (all >0 though) as well). Yet, still, nothing happens when I start, with pump rate maintaining 0. What can I do to solve this? I have no idea what is wrong – we put approx 20 ml of water in the main tube, 20 ml of water for the input tube and an empty one of course for the output.

Any help would be much appreciated! I am very lost as to what is going wrong.

Thanks again.

Best wishes,

Naomi

[harrison]

Hello,

When you click “start” it will probably automatically set the pump rate back to zero, and it won’t necessarily Switch it on.

If you want the pump to run MANUALLY then you need to set the rate to something non zero (like 1) and then click “Switch” on that pump to turn it on.

If you want it to be turned on/off automatically then you need to set it into Turbidostat mode (i.e. “Start” the experiment then click “Regulate OD”) and then provided that the measured OD is less than the OD set-point it will intermittently turn on the pumps.

Does this make sense?

[NaomivdB]

Hi Harrison,

Wonderful, thanks, it is working now! We are looking to add a fixed amount of fresh media and remove volume every 12 hours or so (and no pumping happening in between), could that be arranged with the web interface or will I need to write something in Python for that?

Thanks again

[harrison]

I am afraid if it is going to be that infrequent you will need to do it in the python.
Probably the easiest way to do so would be to add a conditional statement in the main loop of the code (the function runExperiment) which turns the pumps on every 12*60=720 cycles (since each cycle is nominally 60 seconds).
You could to this in a similar way to the function already there to code the terminal which looks like this:

if(sysData[M][‘Experiment’][‘cycles’]%10==9): #Dont want terminal getting unruly, so clear it each 10 rotations.
clearTerminal(M)

In your case you would want it to happen every 720 cycles (i.e. set the top line to have %720=1 or something) and then when that condition is true, set the pump rates to whatever you want and switch them on, and if the condition is false (i.e. add an else statement below it) turn the pumps off.

[NaomivdB]

Thanks so much – that makes a lot of sense and should not be too difficult. Thanks a lot for your quick responses and help!

[harrison]

No worries.
One practical problem you may encounter would be that the pumps will need calibrating to make sure they are injecting the same amount of media as each other. Without this I would guess it might vary by up to 50% between pump heads, since the pumps used are the cheapest ones available!

[harrison]

Something else occured to me as a potentially strategy: If instead of turning the PUMPS on every 12 hours, you might do better to turn on the OD Regulation function even 12 hours, and have it set to (for example) try to reduce the OD to half of whatever it’s value is at that time. Then, have it do a check that turns off the regulation once that target is reached. This way, the pumps will always provide an appropriate amount of liquid (i.e. in terms of factor of dilution), which you would not achieve by just setting them to a fixed flow rate for a fixed amount of time.

[NaomivdB]

Thank you Harrison. We wondered that with that strategy, if, with non-calibrated pumps, you would risk overflow or loss of volume over time, since we will run this experiment for at least a week continuously. Also, do you have more detailed documentation of the Python code? Thanks!

[harrison]

If you run with my second suggestion (using turning on the RegulateOD function) then those things wont be an issue – it shouldn’t overflow or reduce volume.

We do not have a dramatically more documented version, if you want to learn more best bet is looking at the comments, description in the Supplementary Information of the paper about the platform in PLOS Biology, and the user guide. Making more documentation has been on my to do list, but it never reaches a very high position by the time other items come to overtake it…

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