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

biosimulators-utils

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

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.

myokit

A modeling and simulation tool for cardiac cellular electrophysiology

graphein

Protein Graph Library

itolapi

Python API for the Interactive Tree of Life (iTOL)

glycowork

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

codontransformer

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

biosimulators-test-suite

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

kisao

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

finaletoolkit

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

qc-iodata

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

tangram-sc

Spatial alignment of single cell transcriptomic data.

natal-core

Numba-Accelerated Toolkit for Analysis of Lifecycles

toolchest-client

Python client for Toolchest

scphylo-tools

A python toolkit for single-cell tumor phylogenetic analysis

molgraph

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

codon-bias

Python package of codon usage bias analysis tools

chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

pdbe-arpeggio

Arpeggio calculates interatomic contacts based on the rules defined in CREDO.

biosimulators-copasi

COPASI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container