Systems Biology Python Packages

cobra

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

pymoose

C++ basecode and python scripting interface

petab

Python package for working with PEtab files

sbmlmath

SBML MathML ↔ SymPy

biosimulators-utils

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

kisao

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

pybel

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

pypesto

python Parameter EStimation TOolbox

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.

risk-network

RISK: a next-generation tool for biological network annotation and visualization

micom

Python package to study microbial communities using metabolic modeling.

pybiopax

PyBioPAX: A python implementation of the BioPAX object model

sme

Spatial bio-chemical reaction model editor and simulator

biosimulators-test-suite

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

napistu

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

biomass

A Python Framework for Modeling and Analysis of Signaling Systems

bonesistools

Python toolkit from omics data to executable models

biosimulators-copasi

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

ecell4-base

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

petab-select

Model selection for PEtab

gba

Growth Balance Analysis for Python

metevolsim

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

symident

Structural identifiability of ODE models by Lie symmetries over finite fields

cbmpy

CBMPy is a Python based platform for constraint based modelling and analysis.