Computational Biology Python Packages

biotite

A comprehensive library for computational molecular biology

scikit-bio

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

cobra

COBRApy is a package for constraint-based modeling of metabolic networks.

biopandas

Working with molecular structures in pandas DataFrames

pen-stack

Open infrastructure for genome writing: the Writable Genome (learned safe+durable insertion-site atlas), the Writer Atlas of 33k genome-writing enzymes, an inverse-design Write Planner, and a bridge-recombinase off-target engine. Consolidates 5 prior repos. Pre-registered, blind-validated, single install.

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.

codontransformer

CodonTransformer (2M+ Downloads); The tool for codon optimization, optimizing DNA for protein expression

myokit

Source code, issues, and discussions for Myokit: A tool for cardiac electrophysiology modelling and simulation

biosimulators-utils

Utilities for building standardized command-line interfaces for biosimulation software packages

graphein

Protein Graph Library

glycowork

Package for processing and analyzing glycans and their role in biology.

itolapi

Python API for the Interactive Tree of Life (iTOL)

codon-bias

Python package of codon usage bias analysis tools

finaletoolkit

FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.

tangram-sc

Spatial alignment of single cell transcriptomic data.

molforge

A forge for protein workflows. One Python script, every tool in your stack.

stem-ai

Rubric-based trust evaluator for bio/medical AI repositories with dual-path evidence, governance overlay, and institutional audit outputs.

biosimulators-test-suite

Tool for validating that biosimulation software tools implement the BioSimulators standards for simulators

karyon

Legible, deterministic QC/qualification for bio-AI tool outputs — named-reason contracts + agent skills that compose with NVIDIA BioNeMo.

chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

molgraph

Graph neural networks for molecular machine learning: Implemented and compatible with TensorFlow and Keras.

kisao

Ontology of algorithms for analyzing biological models, their parameters, and their outputs

qc-iodata

Python library for reading, writing, and converting computational chemistry file formats and generating input files.

dotmatch

Fast exact short-DNA known-target assignment for CRISPR guides, barcodes, primers, panels, and whitelists.