biomedal-workcell

This is a repository for the biology robotic Workcell in building 446 at Argonne National Laboratory.

Nodes availible

• Opentrons OT-Flex
• Opentrons OT-2 (two available)
• Precise Flex PF400 Robotic Arm
• Analytik Jena Biometra Thermal Cyclers (96 and 384-well versions)
• BMG VANTAstar Microplate Reader
• Hidex Sense Microplate Reader
• Azenta Automated Microplate Sealer
• Azenta Automated Plate Seal Remover

Current projects

• MEDAL, led by Arvind Ramanathan
• Adaptive Lab Evolution (ALE), led by Nidhi Gupta, Paul Hanke, and Chris Henry
• Autonomous Protein Design, led by Gyorgy Babnigg and Rose Wilton

Dependencies

• You'll need docker installed
  • Make sure on Linux to follow the post installation steps to enable non-root user access
• You'll need Python 3.8 or greater installed to run the Experiment Applications.

Configuration

As much as possible, this workcell is designed to be configured declaratively. This is done with:

• A .env file, which you can create by copying example.env (cp example.env .env on Linux), or by running make init.
  • After creating the .env, check to make sure the values are complete and correct.
• The compose.yaml docker compose file, which defines a "stack" of containers that control your workcell
  • Note: whenever you see ${SOME_VARIABLE_NAME} in the compose file, this value is being taken from the .env
• The Workcell Config in workcell_defs/example_workcell.yaml, which allows you to define WEI specific configuration for your workcell

Building, Running, and Managing your Workcell

General Instructions

• make init to initialize your .env file (check to see that the values are correct)
• docker compose up to start your workcell (docker compose up -d starts it in the background)
• docker compose down to stop a workcell
• docker compose logs -f to view the output

Specific instructions for the Biomedal Workcell

Start nodes running through Windows Powershell

Hidex Sense Microplate Reader:

python C:\Users\RPL\source\repos\hidex_module\src\hidex_rest_node.py --port=2005 --output_path='C:\\labautomation\\data_wei\\proc'

Biometra Thermocyclers (96 and 384 well versions):

python C:\Users\RPL\source\repos\biometra_module\src\biometra_rest_node.py --port=2008

and

python C:\Users\RPL\source\repos\biometra_module\src\biometra_rest_node.py --port=2009 --device=biometra4

BMG VANTAstar microplate reader:

C:\Users\RPL\AppData\Local\Programs\Python\Python312-32\python.exe C:\Users\RPL\source\repos\bmg_module\src\bmg_rest_node.py --port 3003 --output_path "C:\\Program Files (x86)\\BMG\\CLARIOstar\\User\\Data"

Sealer:

python C:\Users\RPL\source\repos\a4s_sealer_module\src\a4s_sealer_rest_node.py --device="COM9" --port='2006'

Peeler:

python C:\Users\RPL\source\repos\brooks_xpeel_module\src\brooks_xpeel_rest_node.py --device="COM12" --port=2007

Start the rest of the nodes and wei service through WSL terminal.

These steps will start the nodes for the OT-Flex, both OT-2s, and the pf400 in addition to starting the wei service.

1. open a wsl terminal

2. cd into the biomedal_workcell folder

    cd biomedal_workcell
   

3. start everything through docker

    docker compose up
   

4. check that everything has started by looking at the dashboard.

   Go to http://localhost:8000/ in a browser. If the rest of the nodes have been started correctly, you will see the nodes in a READY state on the left side of the dashboard.

Experiment Applications

See applications/NIDHI/README.md for instructions on setting up and running the adaptive lab evolution experimental application on the biomedal workcell.