Morbidostat setup

Software
1

I’m trying to design an experiment in which the pioreactor will check the OD every 30 minutes, and if it reaches a certain threshold it will add media with salt. I am trying to build this as a profile but it seems that the YAML code cannot do loops or repeated functions. is there a way around it ?

thanks ahead
Dan

2

Hi @danwe1,

Is this just a chemostat with salty-media instead of regular media? Or is there also a regular chemostat operating, and you want to add this additional dosing in? I’ll assume the latter:

There is the repeat action you can use. Here’s a sketch of what if might look like (untested)

common:
  add_alt_media:
     actions:
        type: repeat
        hours_elapsed: 0
        repeat_every_hours: 0.5
        actions:
           type: start
           if: ${{::od_reading:od1.od_reading > 0.5}}
           options:
              mL: 1.0

We aren’t removing waste, so be cautious about overflows. However, if a regular chemostat is running, it will remove extra waste, so it may keep the volume constant. (dependent on your chemostat configuration).

Does that solve your issue?

Another approach is a custom automation, which is also a good idea.

3

Thank you for the quick response! You assumed correctly. I want to add an additional dosing-in every few hours, or when OD reaches a certain threshold, in addition to a turbidostat.
Yet, it seems that there is no such command as repeat_every_hours in the YAML code in “profiles”

4

Hm, I’m not sure what you mean. Are you using a relatively recent Pioreactor software version? Can you show me what you are seeing?

5

I now realized that there is a built-in morbidostat in the program. thank you for your help! I will let you know about any future issues.

6

There is! But it’s not time-based like your original message, nor is it the original “morbidostat” algorithm using thresholds, it’s a dynamic PID approach like what the eVOLVER folks did.

7

The PID approach is even better for my needs. The only thing is, I want to have a record of the salt concentration in the pioreactor over time. is there a way to add this to the morbidostat program?

8

Mmm the closest thing I can suggest is to display the fraction of alt-media, which is proportional to the salt concentration. Try something like this: Morbidostat PID algorithm, tuning, and suggestions - #3 by CamDavidsonPilon to display a chart in your UI.

The raw fraction of alt-media data is in the database, too. You can export it from the UI.