Biology Python Packages

pytdc

Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science

pyfastx

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

deepchem

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

pertdb

Registries for perturbations and their targets.

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

pydna

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

splicecraft

Terminal-based plasmid map viewer, sequence editor, and cloning/mutagenesis workbench in pure Python

bluecellulab

Biologically detailed neural network simulations and analysis API

cogent3

Comparative Genomics Toolkit 3

natal-core

Numerical Aggregation Toolkit for Analysis of Lifecycles

pybioclip

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

rosettapy

A Python utility for wrapping Rosetta command line tools.

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.

pioreactor

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

helical

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

attest-py

A claim-native database for building reality models

ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

pywikipathways

Python Client Package for WikiPathways

bioiain

Toolbox for structural analysis of proteins.

pybiopax

PyBioPAX: A python implementation of the BioPAX object model

deepchopper-cli

Genomic Language Model Mitigates Chimera Artifacts in Nanopore Direct RNA Sequencing

operon-ai

Biologically Inspired Architectures for EpiAgentic Control

ghini-desktop

plant collections manager (desktop version)