Turbidostat doesn't recognize removed volume

Using the Pioreactor
1

Hey everyone,
i’ve tried to use the turbidostat dosing automation. It works fine, until the added volume reaches the number defined in max_volume_ml. Then the dosing automation is stopped with “Vial is calculated to have a volume of 19 mL. Is this expected?”. This is somehow puzzling, due to the turbidostat automation also removing the volume it is designed to. Manually removing volume via the dosing tab doesn’t help either. If the pioreactor is removed and added again to the experiment, the automation works as intended until max_volume_ml is reached.
Both reactors are on 24.10.29, with updates available to 24.12.5.
Has anyone else encountered this problem, or has it already been fixed in 24.12.5?

The relevant parts of my config.ini:

[bioreactor]

max_volume_ml=19.5
initial_volume_ml=17.0
initial_alt_media_fraction=0.5

[dosing_automation.config]
pause_between_subdoses_seconds=5
waste_removal_multiplier=2
max_volume_to_stop=19.5
max_subdose=1.0

As usual, thanks for your help.
Cheers,

2

This warning is produced when your volume is close to the max_volume_to_stop config setting (0.95 * max_volume_to_stop is the threshold to warn). And since your max_volume_ml is 19.5, the Pioreactor will assume you’re adding media up to 19.5, and then the waste tube is reached. So you’ll always go past this warning threshold.

Do you want your max_volume_ml to be equal to max_volume_to_stop? This is a bit strange, and likely will cause problems later. Normally max_volume_ml is close to initial_volume_ml.

Also, am I lacking good documentation on what these values even mean?

3

Hey, thanks as usual for your quick reply. A dumb question at the beginning: Haven’t these values been added via an update? I saw them the first time after the last and assumed they were a new part of the configuration.
So, if i understood you correctly: max_volume_to_stop should be the maximum capacity of the vial, in my case 19.5 mL. max_volume_mL on the other hand is the maximum reachable volume if the waste pump is run continuously, in my case 18 mL.
Is the config.ini and the possible configuration variables documented somewhere? I searched the official docs and came up short.

4

These ones are pretty old, maybe they were missed.

So, if i understood you correctly: max_volume_to_stop should be the maximum capacity of the vial, in my case 19.5 mL. max_volume_mL on the other hand is the maximum reachable volume if the waste pump is run continuously, in my case 18 mL.

That’s correct!

Is the config.ini and the possible configuration variables documented somewhere? I searched the official docs and came up short.

Kinda. The documentation is scattered around our docs. However, these values under bioreactor and dosing_automation.config are quite useful, so we should document them in the docs.

5

These config values are now better documented: Dosing automations | Pioreactor Docs

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