LLTP Config Schema Reference

Project compose for Lab-in-the-Loop runs. lltp.yaml names connectors, auth env vars, and experiments. It is not the LLTP wire protocol (orders, catalogs, status envelopes). Those live in the LLTP spec.

Create a starter file with biolm lab init. Discovery walks from the current directory upward until it finds lltp.yaml. See Lab-in-the-Loop (LLTP) for install, submit/status/results, and the SeqFrame bridge.

Minimal example

yaml

version: 1
default_connector: adaptyv
connectors:
  adaptyv:
    auth:
      token_env: ADAPTYV_API_TOKEN
    defaults:
      service_id: adaptyv-lltp.expression-v1
experiments:
  express:
    connector: adaptyv
    service_id: adaptyv-lltp.expression-v1

Recommended example

yaml

version: 1
default_connector: adaptyv
connectors:
  adaptyv:
    auth:
      token_env: ADAPTYV_API_TOKEN
    defaults:
      service_id: adaptyv-lltp.expression-v1
  twist:
    auth:
      token_env: TWIST_END_USER_TOKEN
      jwt_env: TWIST_STAGING_JWT_TOKEN
      email_env: TWIST_STAGING_USER_EMAIL
    defaults:
      service_id: twist-lltp.dna-synthesis-v1
      wait_for_scoring: false
experiments:
  express:
    connector: adaptyv
    service_id: adaptyv-lltp.expression-v1
  synthesize:
    connector: twist
    service_id: twist-lltp.dna-synthesis-v1
    wait_for_scoring: false

Top-level fields

version — integer; currently 1 (default when omitted).
default_connector — connector name used when submit does not name one (and no experiment supplies it).
connectors — map of connector name → connector config (see below).
experiments — map of experiment name → experiment config (see below).

Connectors

Each entry under connectors is a named lab provider package (for example adaptyv or twist from lltp-connectors).

auth — credentials and env-var pointers (see Auth).
defaults — parameters merged into every submit for this connector unless an experiment or call overrides them. Common keys:
- service_id — connector service identifier (required for most submits).
- wait_for_scoring — Twist-style option; connector-specific.

Other keys under defaults are passed through to the connector.

Experiments

Named presets for biolm lab submit --experiment / biolm.lab.submit(..., experiment=...).

Required

connector — key into connectors.

Optional (and any extra keys)

Everything except connector becomes experiment params. Typical fields:

service_id — overrides connector defaults.service_id.
wait_for_scoring — overrides connector default when present.

Auth

Auth is BYOK. Environment variables always win over inline secrets when the corresponding *_env key is set.

Supported auth keys (inline / env pair):

token / token_env — API token (Adaptyv and similar).
jwt / jwt_env — Twist JWT.
email / email_env — Twist user email.
end_user_token / end_user_token_env — Twist end-user token.

Prefer *_env so secrets stay out of the YAML file.

What is not in this file

Run history and status — stored under .biolm/lltp/.json.
LLTP wire envelopes (orders, catalogs, results) — see the LLTP spec and language SDKs (lltp-py, lltp-js).
SeqFrame Parquet layout — SeqFrame Metadata Schema Reference.

Python

python

from biolm.lab.config import load_config, write_example_config

write_example_config("lltp.yaml")  # or: biolm lab init
cfg = load_config()
print(cfg.default_connector, list(cfg.experiments))