Transformation and PUDU Protocol Chain

Use case

You have run level-1 assembly and want to:

• transform the assembled product into a chassis strain,

• generate PUDU-compatible transformation JSON,

• generate PUDU assembly, transformation, and plating protocols, and

• simulate the full OT-2 handoff chain.

Notebook

The full executable example lives in:

notebooks/buildcompiler_transformation_quickstart.ipynb

It produces artifacts in:

notebooks/results/buildcompiler_transformation_quickstart/

BuildCompiler transformation

After running assembly_lvl1, pass the structured assembly products directly to BuildCompiler.transformation:

transformation_result = compiler.transformation(
    assembly_products,
    chassis_name="E_coli_DH5alpha",
    transformation_doc=assembly_doc,
)

transformation_spec = transformations_to_pudu_json(
    strain_identities=[
        artifact["transformed_strain_module"]
        for artifact in transformation_result["sbol_artifacts"]
    ],
    chassis_identities=["https://sbolcanvas.org/DH5alpha/1"],
    plasmid_sets=[
        [product.plasmid_definition.identity]
        for product in assembly_products
    ],
)

PUDU transformation spec:

[
  {
    "Strain": "http://buildcompiler.org/E_coli_DH5alpha_with_standard_GFP_transformation_lvl1/1",
    "Chassis": "https://sbolcanvas.org/DH5alpha/1",
    "Plasmids": [
      "http://buildcompiler.org/standard_GFP_transformation_lvl1/1"
    ]
  }
]

PUDU protocol generation

PUDU’s documented handoff is:

assembly_input.json
   -> opentrons_simulate assembly_protocol.py
   -> transformation_input.json
   -> opentrons_simulate transformation_protocol.py
   -> plating_input.json
   -> opentrons_simulate plating_protocol.py
   -> plating_layout.json / plating_layout.xlsx

The notebook uses PUDU’s Python API:

from pudu.generate_protocol import detect_protocol_type, generate_protocol

assembly_protocol = generate_protocol(
    protocol_data=assembly_pudu,
    protocol_type="assembly",
    assembly_subtype="SBOL",
)

transformation_protocol = generate_protocol(
    protocol_data=transformation_spec,
    protocol_type="transformation",
    plasmid_locations=plasmid_locations,
)

plating_protocol = generate_protocol(
    protocol_data=plating_input,
    protocol_type="plating",
)

The CLI equivalent is:

python -m pudu.generate_protocol assembly_input.json -o assembly_protocol.py --protocol-type assembly
opentrons_simulate assembly_protocol.py

python -m pudu.generate_protocol transformation_spec.json -o transformation_protocol.py --protocol-type transformation --plasmid-locations transformation_input.json
opentrons_simulate transformation_protocol.py

python -m pudu.generate_protocol plating_input.json -o plating_protocol.py --protocol-type plating
opentrons_simulate plating_protocol.py

Generated files

The validated notebook run generated:

• pudu_assembly_protocol.py

• transformation_input.json

• pudu_transformation_protocol.py

• plating_input.json

• pudu_plating_protocol.py

• plating_layout.json

• plating_layout.xlsx

The final plating input shape matches PUDU:

{
  "bacterium_locations": {
    "A1": [
      "E_coli_DH5alpha_with_standard_GFP_transformation_lvl1",
      "Competent_Cell_DH5alpha",
      "standard_GFP_transformation_lvl1",
      "Media_1"
    ]
  }
}