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

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

codontransformer

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

stem-ai

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

graphein

Protein Graph Library

glycowork

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

biosimulators-test-suite

Tools for validating that biosimulation tools are consistent with the BioSimulators standards

finaletoolkit

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

itolapi

Python API for the Interactive Tree of Life (iTOL)

chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

codon-bias

Python package of codon usage bias analysis tools

kisao

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

proteinfp

End-to-end protein function prediction from structure alone: active sites, binding pockets, GO terms, PPI partners, and drug candidates.

tangram-sc

Spatial alignment of single cell transcriptomic data.

toolchest-client

Toolchest Python client

molgraph

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

biosimulators-copasi

BioSimulators-compliant command-line interface to the COPASI simulation program <http://copasi.org>.

biomass

A Python Framework for Modeling and Analysis of Signaling Systems

biosimulators-tellurium

BioSimulators-compliant command-line interface to the Tellurium/roadrunner simulator <https://tellurium.readthedocs.io/>.