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 - 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.
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file lamindb-0.50.7.tar.gz.
File metadata
- Download URL: lamindb-0.50.7.tar.gz
- Upload date:
- Size: 266.2 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: python-requests/2.31.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 6ce63753ed46d512de9adcfde6dea39f5c5b3cac1ae715e6cda1435762aae5a9 |
|
| MD5 | 8686c2f9ada3d761f86395455494cd63 |
|
| BLAKE2b-256 | 761da5267d0d739e157e04b0924a1ffba2d923b56a673715394790a393fc6f63 |
Provenance
File details
Details for the file lamindb-0.50.7-py3-none-any.whl.
File metadata
- Download URL: lamindb-0.50.7-py3-none-any.whl
- Upload date:
- Size: 80.0 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: python-requests/2.31.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | f7e22cda23b063e4d8093e16f6ccb19875f5c5a5060e163f7d758df830171845 |
|
| MD5 | 8085a9171a5ff6af01d114702426df57 |
|
| BLAKE2b-256 | d05542b7414366fbe5663498fe99a62d3db1329780d0662f08e68dedd4eb7408 |
