I have a question about the turbidostat settings. In the dosing menu, the Time between check setting is greyed out and set to 0.25 minutes. I can however edit this setting after I have started the turbidostat. Is there a reason for this? It would be more convenient to set it directly at the start.
Ah, that’s a bit of a artifact that we need to fix. I believe even if you tried to edit it afterwards, it wouldn’t update and stay at 0.25.
Okay I see! Good to know, I’ll check it next time.
I’m having issues with Turbidostat when using it as part of a profile.
When Turbidostat starts running I notice it removes waste twice every time it adds media. Effectively it’s reducing the vail volume by double the Turbidostat increment every time it cycles. I don’t understand why Turbidostat would ever do that. As Turbidostat continues the UI thinks it has reached the max volume after enough cycles (which makes no sense since the UI seems recognizes it is removing more volume than it’s adding, based on the logs). In reality it has empty the vial (and the last few OD readings are all over the place, above and below target value). See logs for pumping
I call the Turbidostat automation in my profile like this:
…
dosing_automation:
actions:
- type: start
hours_elapsed: 0.056
options:
automation_name: turbidostat
target_od: 3
duration: .01
exchange_volume_ml: 15
- type: stop
hours_elapsed: 0.195
…
I’m not sure if this script is correct… I used this as a reference Turbidostat after time - #2 by CamDavidsonPilon
I couldn’t find any more formal instructions on how to write the code. As I understand it “exchange_volume_mL” is the total amount of media Turbidostat can add to the vail to achieve target OD.
NOTE: In this profile I’m not using Turbidostat to just maintain OD but to dilute the media to a specific OD from a pure, the important information being the volume of media needed to dilute to the OD
So there is a very specific reason why for regular operation of a turbidostat (see here), but in your case, you can turn if off by changing waste_removal_multiplier under [dosing_automation.config] to 0.
As Turbidostat continues the UI thinks it has reached the max volume after enough cycles
I’m curious where you are seeing this. Is it a log that pops up?
As I understand it “exchange_volume_mL” is the total amount of media Turbidostat can add to the vail to achieve target OD.
will add, not just can.
NOTE: In this profile I’m not using Turbidostat to just maintain OD but to dilute the media to a specific OD from a pure, the important information being the volume of media needed to dilute to the OD
I think the regular turbidostat will still work, even with low exchange_volume_ml. It will check every 30 seconds, and if OD > target OD, exchange exchange_volume_ml, then repeat again in 30 seconds. Eventually this will converge to your target OD. Am I understanding correctly?
Thanks Cam.
I had forgotten that detail about the pump running extra to maintaining a constant volume (it had been a long week) but I never knew I could over ride that! Very helpful.
Now that I have a bit more of an understanding of the code from what you said, and updated info here Experiment profile schema and syntax | Pioreactor Docs it might be possible for Turbidostat to work if I can figure out how to track the dilution Turbidostat runs and use that to calculate density from the volume added.
Is there a lower limit to how short the duration can be between Turbidostat cycles (<=0.001hr or 0)?
Unfortunately I haven’t been able to test using Turbidostat further because the UI is not recognize any removing of liquid. I tried this but no luck Pioreactor not accounting for removed volume in turbidostat automation and hitting maximal volume and cancelling automation
max working volume = 15
Any suggestions? The only way I can get the UI volume down is rebooting the pioreactor (the manual initiated pumping or volume override in the dosing controls don’t seem to have effect) - Might need a new topic for the issues with the volume tracking
I think it would more logical for me to just write code to determine density directly (using a titration style dilution to a predetermined OD for more accuracy) and handle the liquid movement etc. but I haven’t had any success writing the code with my limited coding experience so I’m continuing to follow the advice I’ve gotten and trying to patch something together using existing dosing automations (which brings up new challenges of understanding the intricacies of the automations’ code and syntax)