lamindb 0.51a1

Open-source data platform for biology.

LaminDB - Open-source data platform for biology

Public beta: Close to having converged a stable API, but some breaking changes might still occur.

LaminDB is a Python library to manage data & analyses related to biology:

• Track & query data lineage across pipelines, notebooks & app uploads.
• Query, validate & link data batches using biological registries & ontologies.
• Manage features & labels schema-less or schema-full.
• Collaborate across a mesh of LaminDB instances.

If you want a UI: LaminApp is built on LaminDB. If LaminDB ~ git, LaminApp ~ GitHub.

(LaminApp, support, integration tests & schemas for an enterprise platform are available on a paid plan - on-prem or hosted by us.)

Quickstart

Installation and sign-up take no time: Run pip install lamindb and lamin signup <email> on the command line.

Init a LaminDB instance with local or cloud default storage like you'd init a git repository:

$ lamin init --storage ./mydata   # or s3://my-bucket, gs://my-bucket

Validate & register a DataFrame:

import lamindb as ln
import pandas as pd

ln.track()  # track run context in a notebook

df = pd.DataFrame({"feat1": [1, 2], "feat2": [3, 4], "perturbation": ["pert1", "pert2"]})

ln.File.from_df(df, description="Data batch 1").save()  # create a File object and save/upload it

Query & use a DataFrame:

ln.File.search("batch 1")  # run a search

file = ln.File.filter(labels="pert1").one()  # or a query (under-the-hood, you have the full power of SQL to query)

df = file.load()

Documentation

Read the docs.