GPT to create experiment profiles

Using the Pioreactor Advanced users
1

I’ve been playing with a custom GPT to create experiment profiles for the Pioreactor. Check this out:

Try asking it something like:

Create a profile that starts stirring immediately in all Pioreactors, then changes the RPM to 400 after 5 minutes, and another 50 RPM every 5 minutes after that, for 1 hour in total. Then stop stirring.

Here’s my chat log … and it works!

Screenshot 2023-11-09 at 8.59.15 PM
Screenshot 2023-11-09 at 8.59.15 PM2486×1304 240 KB

It’s often wrong about what options are available for a job, but that’s something I can fix once I upload some more data to it about options.

2 Likes
2

Nice, would you embed this in the web interface so we don’t even need to copy & paste the output?

3

Ooh I didn’t realize one needs chatgpt plus to use this =(

4

I decided to check it out. I tried using this prompt:

Create a profile. At start, stirring, temperature, and dosing will start. Start temperature is 35 C for all bioreactors. After 24 hours, the temperature in pio-dev-00 will increase by 2 C every two hours until it reaches a maximum of 50 C, after which the temperature stays constant. After 24 hours, the temperature in pio-dev-01 will increase by 1 C every two hours until it reaches a maximum of 50 C, after which the temperature stays constant. After 24 hours, the temperature in pio-dev-02 will increase by 4 C every four hours until it reaches a maximum of 50 C, after which the temperature stays constant.

And I got this:

experiment_profile_name: multi_bioreactor_temperature_ramp

metadata:
  author: realPeteDavidson
  description: This profile starts with stirring, temperature control, and dosing. After 24 hours, temperature increases at different rates for pio-dev-00, pio-dev-01, and pio-dev-02 until a maximum of 50°C is reached.

common:
  stirring:
    actions:
      - type: start
        hours_elapsed: 0.0
  temperature_control:
    actions:
      - type: start
        hours_elapsed: 0.0
        options:
          automation_name: thermostat
          target_temperature: 35
  dosing:
    actions:
      - type: start
        hours_elapsed: 0.0

pioreactors:
  pio-dev-00:
    jobs:
      temperature_control:
        actions:
          - type: update
            hours_elapsed: 24.0
            options:
              target_temperature: 37
          - type: update
            hours_elapsed: 26.0
            options:
              target_temperature: 39
          # Repeat this pattern until reaching 50°C
          - type: update
            hours_elapsed: 46.0
            options:
              target_temperature: 50

  pio-dev-01:
    jobs:
      temperature_control:
        actions:
          - type: update
            hours_elapsed: 24.0
            options:
              target_temperature: 36
          - type: update
            hours_elapsed: 26.0
            options:
              target_temperature: 37
          # Repeat this pattern until reaching 50°C
          - type: update
            hours_elapsed: 50.0
            options:
              target_temperature: 50

  pio-dev-02:
    jobs:
      temperature_control:
        actions:
          - type: update
            hours_elapsed: 24.0
            options:
              target_temperature: 39
          - type: update
            hours_elapsed: 28.0
            options:
              target_temperature: 43
          # Repeat this pattern until reaching 50°C
          - type: update
            hours_elapsed: 44.0
            options:
              target_temperature: 50

It’s nice having it create the structure and formatting.

Edit: added code block

5

# Repeat this pattern until reaching 50°C

sigh haha

I tried this prompt, and had to beg to explicitly get the GPT to write them all out. I’ve made some changes to the GPT to hopefully help.

This is a very good example prompt + profile output, so I’ve included the pair in the GPT, too.

FYI I did find a bug in our profile verify code, so you pio update app -b develop to get the fix if you encounter a ValueError: Update automations, not controllers error. EDIT: corrected

6

I’m receiving the ValueError and tried updating using “pio update -b develop”.

I’m receiving this error (in the SSH terminal):

Usage: pio update [OPTIONS] COMMAND [ARGS]…
Try ‘pio update --help’ for help.
Error: No such option: -b

Also, if I’m running 3 leader_worker images on the cluster, should I be running: (1) “pio update -b develop” on the leader only; (2) “pio update -b develop” on each leader and follower in the cluster; or (3) “pios update -b develop” on the leader?

edit: I figured it out, it’s actually “pio update app -b develop”. I updated it via the *.local/updates GUI page, but I am still curious about the second question I had (pio vs pics).

edit2: I’m still getting that error after updating to the develop version. I’m running on the “Preview Profile” mode.

When I run your example, it works without issue:

experiment_profile_name: demo_stirring_example

metadata:
  author: Cam Davidson-Pilon
  description: A simple profile to start stirring in your Pioreactor(s), update RPM at 90 seconds, and turn off after 180 seconds.

common:
  stirring:
    actions:
      - type: start
        hours_elapsed: 0.0
        options:
          target_rpm: 400.0
      - type: update
        hours_elapsed: 0.025
        options:
          target_rpm: 800.0
      - type: stop
        hours_elapsed: 0.05

This runs in “Preview Profile” without issue.

This second code gives me the red error:

experiment_profile_name: multi_bioreactor_temperature_ramp

metadata:
  author: realPeteDavidson
  description: This profile starts with stirring, temperature control, and dosing. After 24 hours, temperature increases at different rates for pio-dev-00, pio-dev-01, and pio-dev-02 until a maximum of 50°C is reached.

common:
  stirring:
    actions:
      - type: start
        hours_elapsed: 0.0
  temperature_control:
    actions:
      - type: start
        hours_elapsed: 0.0
        options:
          automation_name: thermostat
          target_temperature: 35
  dosing:
    actions:
      - type: start
        hours_elapsed: 0.0

pioreactors:
  pio-dev-00:
    jobs:
      temperature_control:
        actions:
          - type: update
            hours_elapsed: 24.0
            options:
              target_temperature: 37
          - type: update
            hours_elapsed: 26.0
            options:
              target_temperature: 39
          # Repeat this pattern until reaching 50°C
          - type: update
            hours_elapsed: 46.0
            options:
              target_temperature: 50

  pio-dev-01:
    jobs:
      temperature_control:
        actions:
          - type: update
            hours_elapsed: 24.0
            options:
              target_temperature: 36
          - type: update
            hours_elapsed: 26.0
            options:
              target_temperature: 37
          # Repeat this pattern until reaching 50°C
          - type: update
            hours_elapsed: 50.0
            options:
              target_temperature: 50

  pio-dev-02:
    jobs:
      temperature_control:
        actions:
          - type: update
            hours_elapsed: 24.0
            options:
              target_temperature: 39
          - type: update
            hours_elapsed: 28.0
            options:
              target_temperature: 43
          # Repeat this pattern until reaching 50°C
          - type: update
            hours_elapsed: 44.0
            options:
              target_temperature: 50

Running this code in “Preview Profile” gives me the following error: “Update automations, not controllers, with settings.”

7

pios update -b develop is syntactical-sugar for running pio update -b develop on all the workers (which in your case, includes your leader since it doubles as a worker). This is generally true: pios x runs pio x on all the workers.

In this case, since the profile logic runs only on the leader, you only need to update the leader, so pio update app -b develop is sufficient.

BTW the profile you posted above does have some valid errors, so I would suggest trying the GPT again. Basically it should look something like this.

8

Thanks. I’ll check out the other examples you’ve uploaded as well and play around with them.