LaminDB: Manage R&D data & analyses.

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LaminDB: Manage R&D data & analyses

LaminDB is an open-source data lake for biology.

It gives you components to build on data lineage & biological entities with an ORM for your existing infrastructure: object storage (local directories, S3, GCP) with a mapped SQL query engine (currently: SQLite, Postgres).

You can create distributed LaminDB instances at any scale:

  • Get started on your laptop, deploy in the cloud, or work with a mesh of instances for different teams and purposes.
  • Share them through a hub akin to HuggingFace & GitHub - see, e.g, lamin.ai/sunnyosun.
Public beta: Currently only recommended for collaborators as we still make breaking changes.

Update 2023-06-05: We completed a major migration from SQLAlchemy/SQLModel to Django, available in pre-release of v0.42.

Installation

LaminDB is a Python package (Python 3.8+).

pip install lamindb

It is configurable & works with custom schema modules (each being managed as a Django app):

pip install 'lamindb[bionty]'  # install biological entities
pip install 'lamindb[nbproject]'  # install Jupyter notebook tracking
pip install 'lamindb[aws]'  # install AWS dependencies (s3fs, etc.)
pip install 'lamindb[gcp]'  # install GCP dependencies (s3fs, etc.)

Setup

Quick setup on the command line:

  • Sign up via lamin signup <email>
  • Log in via lamin login <handle>
  • Set up an instance via lamin init --storage <storage> --schema <schema_modules>

Documentation

Read the docs.

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