Running Protocols Locally

CLI: biolm protocol run-local

biolm protocol run-local my_protocol.yaml --input sequence=MKLLIV
biolm protocol run-local my_protocol.yaml --input sequences='["MKLLIV","MKTAY"]' --json

--input accepts key=value pairs. Values are parsed as JSON when possible (lists, numbers, booleans); otherwise they are treated as plain strings. Use --json to print the full records list. Use --output-dir to set the pipeline DuckDB cache directory.

For hosted platform runs of a registered protocol slug, use biolm protocol run SLUG instead — see Running Protocols on the Platform.

Python: Protocol.execute()

from biolm.protocols import Protocol

protocol = Protocol("my_protocol.yaml")
result = protocol.execute(inputs={"sequence": "MKLLIV"})

print(result.run_id)
print(result.records)           # list[dict] — all rows
print(result.selected_records)  # rows matching outputs[] rules (if any)
print(result.dataframe)         # pandas DataFrame

The convenience function run_local_protocol() accepts a parsed protocol dict instead of a file path.

Results and outputs[] selection

After a local run, LocalRunResult exposes:

• records — every row from the final pipeline DataFrame (JSON-safe dicts).

• selected_records — union of rows selected by the protocol’s outputs[] rules (where, order_by, limit), using the same logic as MLflow protocol logging.

• output_selections — per-rule breakdown (rule_index, rule, records).

Example protocol snippet:

outputs:
  - where: "${{ mean_plddt > 70 }}"
    order_by:
      - field: mean_plddt
        order: desc
    limit: 10

result = protocol.execute(inputs={"sequences": ["MKLLIV", "MKTAY"]})
top = result.selected_records
for rule_sel in result.output_selections:
    print(rule_sel.rule_index, len(rule_sel.records))

SeqFrame bridge (optional)

If you have the seqframe extra installed, materialize results as a SeqFrame:

sf = result.to_seqframe()  # requires pip install "biolm[seqframe]"

Unsupported features

Protocols using gather, foreach, subtasks, non-ApiTask runners, or tasks. expressions in templates fail fast at compile time with UnsupportedProtocolFeature. See Local Protocol Profile v1 for the full matrix.

See also

• Local Protocol Profile v1 — Local Protocol Profile v1 reference

• Authoring and Validating Protocols — validate before running

• biolm.protocols — API reference

• biolm protocol — CLI options for run-local