http://www.bioartbot.org/

BioArtBot Robotic Artist from Counter Culture Labs

This project provides an interface for users to draw and submit pixel art via a web app, and then converts that submission into instructions for an Opentrons OT2 robot to reproduce that drawing by distributing colorful micobes onto an agar plate. As the microbes grow, the picture comes into focus, resulting in living art. It's very neat.

The code breaks into three sections, each of which can be run independently:

• Web app to create drawings
• Translation code to produce instructions for the robot
• Lab protocols to grow color-producing microbes

Web

prerequisites

• Install Docker compose

to run locally

docker-compose up -d --build                                       # build and spin up containers
docker-compose exec artbot flask db upgrade                                 # setup database

to inspect the database

docker-compose exec artbot-db psql -U postgres -d artbot_dev

to access the application

• go to localhost:5001 for the web interface
• go to localhost:1080 for the mail-dev client (inspect outgoing e-mails)

if you contribute code

Changes to the data models must be accompanied by a migration script which you can generate by running:

docker-compose exec artbot flask db migrate -m "short description"

The script will be created in migrations/versions. Please inspect the file, change it if required, and test it by running:

docker-compose exec artbot flask db upgrade
docker-compose exec artbot flask db downgrade                   # check backward compatibility

Use the logs to check for any errors during the migration:

docker-compose logs arbot

Troubleshooting

Trouble generating the migration script

Might require updating the migrations/versions folder permissions, to give Docker write access

chown :1024 migrations/versions                 # set group permissions to gid shared with docker

Screenshot

Robot

To run:

With the web containers running, execute these commands:

mkdir robot/procedures
chown :1024 robot/procedures
docker-compose exec artbot python run_procedure_generator.py

The generated procedure will be timestamped and saved in procedures folder

To upload generated procedure to robot:

• Download official Opentrons app
• First time only: upload custom_artbot_labware.py using OT app
• Upload generated procedure (this will take awhile)
  • Use this time to gather materials for the procedure - see "Lab" section below
• Callibrate as normal, but when calibrating "Canvas" labware, calibrate to top of lid, approximately 10mm from the upper edge and 15mm from the left edge
  • This provides a margin for the microbial growth to spread out a little

If everything works correctly, the pipette tip will just pierce the agar for each pixel it places. This is done on purpose - since it's hard to get precise volume for each agar plate, we just overestimate.

Troubleshooting

If the pipette tip misses your agar, it's easiest to troubleshoot using the Jupyter Notebook server that the OT2 runs to interact with the robot. In fact, you can generate the template in a Jupyter Notebook instead with python3 art_processor.py --notebook. Once you know the correct distance between the top of the lid and the agar, change it in ART_TEMPLATE.txt

Lab

Materials:

• Opentrons OT2 Liquid Handling Robot
• 6-well 15mL tissue culture plates for liquid culture 'palette'
• Omni-tray plates for canvases - one per artpiece
• Standard 200ul tiprack

Procedure in brief:

• In a sterile environment:
  • Pour LB agar with into omni-tray plates
  • Transfer 5-10 mL of liquid color-producing e. coli culture into a 6-well plate
• Follow instructions in OT app upon upload of procedure