Systems Biology Python Packages

cobra

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

pybel

🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)

petab

Python package for working with PEtab files

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.

sbmlmath

SBML MathML ↔ SymPy

biosimulators-utils

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

pybiopax

PyBioPAX: A python implementation of the BioPAX object model

bonesistools

Python-implemented toolkits for upstream and downstream analyses around the BoNesis ecosystem.

napistu

The core library of the Napitsu project supporting the creation, transformation, and network-based interrogation of biological pathways

micom

Python package to study microbial communities using metabolic modeling.

sme

Spatial bio-chemical reaction model editor and simulator

pypesto

python Parameter EStimation TOolbox

ecell4-base

An integrated software environment for multi-algorithm, multi-timescale, multi-spatial-representation simulation of various cellular phenomena

biosimulators-test-suite

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

petab-select

Model selection for PEtab

stochpy

StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks

kisao

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

pybel-tools

A PyBEL extension for analyzing BEL graphs

bio2bel-wikipathways

Integration of pathway-related information from WikiPathways in BEL

biosimulators-copasi

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

metevolsim

MetEvolSim (Metabolome Evolution Simulator). A Python package to simulate the long-term evolution of metabolic levels.

gba

Growth Balance Analysis for Python

bonesis

Synthesis and Reprogramming of Most Permissive Boolean Networks

biomass

A Python Framework for Modeling and Analysis of Signaling Systems