Biology Python Packages

deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

pytdc

Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science

opentrons

Software for writing protocols and running them on the Opentrons Flex and Opentrons OT-2

opentrons-shared-data

Software for writing protocols and running them on the Opentrons Flex and Opentrons OT-2

pyfastx

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

splicecraft

In-Terminal Plasmid Design Workbench

cogent3

Comparative Genomics Toolkit 3

pertdb

Registries for perturbations and their targets.

pydna

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.

histolab

Library for Digital Pathology Image Processing

bluecellulab

Biologically detailed neural network simulations and analysis API

indra

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

rosettapy

A Python utility for wrapping Rosetta command line tools.

attest-py

A claim-native database for building reality models

operon-ai

Biologically Inspired Architectures for EpiAgentic Control

helical

A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

wetlab

Registries for perturbations and their targets.

deepchopper-cli

Genomic Language Model Mitigates Chimera Artifacts in Nanopore Direct RNA Sequencing

pybioclip

Python package and CLI that simplifies using the BioCLIP family of foundation models.

pybiopax

PyBioPAX: A python implementation of the BioPAX object model

pioreactor

Hardware and software for accessible, extensible, and scalable bioreactors. Built on Raspberry Pi.

clustergrammer2

"Dimensionality-increasing" data visualization tool and interactive WebGL Jupyter widget built for single-cell data.

attestdb

A brain for AI agents that actually learns — confidence scoring, negative results, gap detection. pip install attestdb && attest brain install

ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers