biocentral

This is the biocentral python package, providing all functionality of the biocentral ecosystem in one package.

Installation

Install from pypi using pip:

pip install biocentral

If you want to deploy your own server, add the server extra:

pip install biocentral[server]

If you want to run local functionality, add the local extra:

pip install biocentral[local]

Note that local and server install require large dependencies, while the default mode is minimal and lightweight.

Quick Start

1. Create a biocentral object:

from biocentral import Biocentral

biocentral = Biocentral(mode="api")  # or "local"

2. Visualize some data:

from biocentral import BiocentralChart
from biotrainer_core.input_files import read_FASTA

sequence_data = read_FASTA("your_sequences.fasta")

sequence_length_distribution = BiocentralChart.sequence_length_distribution(sequence_data)
sequence_length_distribution.chart.interactive()

3. Embed the sequences via a protein language model:

embeddings = biocentral.embed(embedder_name="Rostlab/ProstT5", sequence_data=sequence_data, reduce=True)
print(embeddings)

Find more examples in the examples directory!

License

This package is subject to the MIT License.