ThomVett / lamindb

Manage R&D data and analyses.

LaminDB: Manage R&D data & analyses

Curate, store, track, query, integrate, and learn from biological data.

LaminDB is an open-source data lake for R&D in 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 (SQLite, Postgres, and soon, BigQuery).

You can readily 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.

Installation

LaminDB is a python package available for Python versions 3.8+.

pip install lamindb

Biological entities are installed like so:

pip install 'lamindb[bionty,wetlab]'

Import

In your python script, import LaminDB as:

import lamindb as ln

Quick 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.