So this is a very different solution than the one you are attempting, but I think this is how I want users to solve something like this.
Instead of writing a custom dosing-automation, which as you can tell is not easy, I propose writing an experiment profile. A profile is like a script, and in that script, you can run jobs on a scheduale, and even loop actions. You can even have some basic input variables.
But first, we are going to create a new job that can be called from the experiment profile. This job simply wraps some pump logic so it’s easy to run a command like:
pio run pumps --media 10 --waste 12
which will, as you might guess, run media for 10ml and then run waste for 12ml.
However, in a profile, we specify the job-name (pumps), and the options. Consider the following (simplified) profile:
common:
jobs:
pumps:
actions:
- type: start
hours_elapsed: 0
options:
media: 10
waste: 12
This does the same thing as the pio command above. And we can extend the profile add more actions, logging, etc.
Let’s first add this new job, pumps. (FYI, I like this pumps job so much I’ll be adding it to the core software in the next release).
- SSH into your Pioreactor(s)
- run
nano .pioreactor/plugins/pumps.py
- Copy and paste the following code: pumps.py · GitHub
- Save and exit with ctrl-x
Now all your pioreactors can run a command like:
pio run pumps --media 10 --waste 12
pretty cool!
Next, we’ll add a experiment profile that mimics your goal.
experiment_profile_name: chemostat in OD out 2
metadata:
author: Cam DP
description: "
1. purges media line from photobioreactor (PBR)to pioreactor vial,
2. rinses the vial with alternative media (filtered water),
3. empties vial,
4. fills vial with media (algae in nutrient media) and alt media for a dilution of 1 to 10,
5. takes the OD measurement,
6. empty vial,
7. rinse vial with alt media,
8. empty vial
9. purge waste line with alt media
"
inputs:
media_length: 24
waste_length: 24
common:
jobs:
stirring:
actions:
- type: start
hours_elapsed: 0
dosing_automation:
actions:
- type: start
hours_elapsed: 0
options:
automation_name: silent
pumps:
actions:
- type: repeat
repeat_every_hours: 1
hours_elapsed: 0
actions:
- type: log
hours_elapsed: 0
options:
message: Purging tubing
- type: start
hours_elapsed: 0
options:
media: ${{media_length/12}}
waste: ${{media_length/12 + 1}}
- type: log
hours_elapsed: 0.01666667
options:
message: Rinsing vial
- type: start
hours_elapsed: 0.01666667
options:
alt_media: 18
- type: log
hours_elapsed: 0.0333332
options:
message: Emptying vial
- type: start
hours_elapsed: 0.0333332
options:
waste: 19
- type: log
hours_elapsed: 0.0499998
options:
message: Adding fresh media
- type: start
hours_elapsed: 0.0499998
options:
media: 1.5
alt_media: 15
- type: log
hours_elapsed: 0.05
options:
message: Mixing solution
- type: log
hours_elapsed: 0.0666664
options:
message: Emptying and rinsing
- type: start
hours_elapsed: 0.0666664
options:
waste: 19
alt_media: 18
- type: log
hours_elapsed: 0.083333
options:
message: Emptying and rinsing
- type: start
hours_elapsed: 0.083333
options:
waste: 19
alt_media: ${{ waste_length/12 }}
od_reading:
actions:
- type: repeat
hours_elapsed: 0
repeat_every_hours: 1
actions:
- type: log
hours_elapsed: 0.0583331
options:
message: Taking OD snapshot
- type: start
hours_elapsed: 0.0583331
- type: stop
hours_elapsed: 0.0593331
In your UI, visit the Profiles page, and Create New Profile, and paste this code above. On the right hand side is a high-level view of the profile you can review.
Some notes:
- I’ve put in some input variables,
media_length and waste_length - you can change these as you wish.
- Currently, it runs once an hour, starting when you start the Profile. You can change this in the
repeat block.
- I also couldn’t recreate the
max logic in your Python (there’s no max function in profiles).
The profile also starts stirring, and the silent dosing_automation. This is because when dosing_automation is one, you can get better metrics and visibility into any pump behaviour.
One last thing! I am very concerned with adding 19ml to the vial. Anything above 18ml makes me nervous of an overflow. If a pump hiccups, or slows for some reason, it can cause a disaster. For this application, I would recommend something lower.