biolm model

biolm model build

Build a BioLM definition recipe into a locked local package.

Compiles an embedding_head recipe YAML via Finetune.xgboost and writes ~/.biolm/models///BioLM. The recipe file is not modified.

Usage

biolm model build [OPTIONS] PATH

Options

--tag <tag>

Package tag under ~/.biolm/models/<name>/

Default:

'latest'

--name <model_name>

Override recipe name for the package identity

--bundle

Download head artifact into package artifacts/ (preload)

--artifact <artifact>

Head artifact PATH or URL (required for –bundle if finetune result has no URI)

Arguments

PATH

Required argument

biolm model catalog

List the full open-source model catalog, including every deployable model on the platform.

When connected to biolm-hub, lists gateway routes from OpenAPI instead of the hosted catalog.

Usage

biolm model catalog [OPTIONS]

Options

--format <format>

Output format

Options:

table | json | yaml

-o, --output <output>

Save output to file

biolm model example

Generate copy-pasteable Python SDK examples for a model and action.

Omit model_name to list available models; choose output as Python, Markdown, RST, or JSON.

Usage

biolm model example [OPTIONS] [MODEL_NAME]

Options

-a, --action <action>

Specific action (encode, predict, generate, lookup)

-f, --format <format>

Output format

Options:

python | markdown | rst | json

-o, --output <output>

Output file path (default: stdout)

Arguments

MODEL_NAME

Optional argument

biolm model export mlflow

Export a local BioLM package to an MLflow model directory.

Requires the mlflow-biolm package (pip install mlflow-biolm). PACKAGE is name, name:tag, or a package directory path.

Usage

biolm model export-mlflow [OPTIONS] PACKAGE

Options

-o, --output <output>

Output directory for the MLflow model (default: <package>/mlflow)

Arguments

PACKAGE

Required argument

biolm model list

List available models from the BioLM catalog with filtering, sorting, and export options.

Output can be a Rich table in the terminal or saved as JSON, YAML, or CSV for scripting.

Usage

biolm model list [OPTIONS]

Options

--filter <filter>

Filter models (e.g., encoder=true, model_name=esm2)

--sort <sort>

Sort by field (e.g., model_name, -model_name for descending)

--format <format>

Output format

Options:

table | json | yaml | csv

-o, --output <output>

Save output to file

--fields <fields>

Comma-separated list of fields to display

--view <view>

Predefined field views (enriched includes description, tags, etc.)

Options:

compact | detailed | full | enriched

biolm model run

Run a model action against sequences or structures from files, stdin, or inline JSON.

Supports encode, predict, generate, and lookup with batching, progress output, and common bioinformatics formats (FASTA, CSV, PDB, JSON).

Usage

biolm model run [OPTIONS] MODEL_NAME {encode|predict|generate|lookup}

Options

-i, --input <input>

Input file path or “-” for stdin

-o, --output <output>

Output file path (default: stdout)

--format <format>

Output format (auto-detected from output file extension)

Options:

json | fasta | csv | pdb

--input-format <input_format>

Input format (auto-detected from input file extension)

Options:

json | fasta | csv | pdb

--type <type>

Input type override (sequence, pdb, context, etc.)

--params <params>

Parameters as JSON string or file path

--batch-size <batch_size>

Batch size for processing (default: auto-detect from schema)

--progress

Show progress bar for batch processing

Arguments

MODEL_NAME

Required argument

ACTION

Required argument

biolm model show

Show metadata, actions, and optional JSON schemas for a specific model.

Look up models by slug or display name; use --include-schemas for request/response shapes.

Usage

biolm model show [OPTIONS] MODEL_NAME

Options

--format <format>

Output format

Options:

table | json | yaml

-o, --output <output>

Save output to file

--include-schemas

Include JSON schemas for each action

--include-code-examples

Include code examples from API (fetches detailed model info)

Arguments

MODEL_NAME

Required argument