Changing the cycletime of OD Measurement

[Johanna Spangler]

Hey Harrison,

i have a question about the cycletime in row 49 of the code at github.
I want to couple Chibio with an other System, but to make this work i think i need to change the cyletime.
Has it impacts if i change from 60 s to for example 300 s or 1200 s? Do i need to change other rows too or just this row 49?

Regards
Johanna Spangler

[harrison]

Hello Johanna,

I think the first approach would be to just try it and see what happens.
In terms of potential problems, one might be that the pumpiing and/or temperature control might be impacted. The pumping runs on its own cycle which is set to be longer than the main cycle time, so perhaps you would wish to instead make this a separate time (i.e. keep it 60 seconds) so that the pump runs at similar intervals.
Similarly the temperature control does intermittent measurement and heating which, if you change the timing, might make it less precise. So again, I’d suggest making sure that one is running at a fixed timestep so that you don’t end up with very variable temperatures.

Is there a logistical reason why you really MUST change the cycle time? It might be that you can achieve your goals via some other mechanisms (i.e. leaving the cycle time fixed but telling the code to just not do certain things every cycle).
harrison

[JairD]

I’m interested in doing the same, I want to change the OD lecture time to every 1200 seconds, to keeping the starring the other ~1130 s and I have the sames concerns about the possible affection in heating and pumping. @Johanna do you made it? Anyone have suggestions to modify the interval time of the lectures?

[harrison]

Hello Jair,
Why exactly do you want this? If you are very concerned about stirring not being enough you could just reduce the pause between stirring stopping and the OD measurement.
The easiest (hacky) way to do what you want (if the above is not OK) would be to make the turning off/ON stirring parts of the code only happen 1 in each 20 cycles, and also set the OD reading to be such that it maintains the same value as the last 19 times and only updates once every 20th. But I really don’t understand what you gain by doing fewer OD readings. It will make the whole system much more susceptible to noise, and the OD regulation function will not work particularly well since it is only getting measurements a few times an hour, so likely it will massively over/undershoot the OD target. If you don’t want regular OD readings then just throw them out/average them out after the experiment

[JairD]

Thanks for the reply. I will try your advice.
I want to change the code because we have had some problems growing some mutants when we made batch cultures, and one of our thoughts is that the supply of oxygen is not enough, and this is aggravated by the multiples stops for reading the OD, we hope that keeping the stirring for a longer time improve the growth.

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