Open-source data platform for biology.
Project description
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 - in your or our infrastructure.)
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.
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