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)

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.

petab

Python package for working with PEtab files

sme

Spatial bio-chemical reaction model editor and simulator

sbmlmath

SBML MathML ↔ SymPy

biosimulators-test-suite

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

napistu

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

pybiopax

PyBioPAX: A python implementation of the BioPAX object model

micom

Python package to study microbial communities using metabolic modeling.

kisao

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

metevolsim

MetEvolSim (Metabolome Evolution Simulator) Python Package

pypesto

python Parameter EStimation TOolbox

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

bonesistools

Python package providing bioinformatics tools for upstream and downstream analysis of the BoNesis framework

sccellfie

scCellFie infers metabolic activities from single-cell and spatial transcriptomics and offers a variety of downstream analyses.

biosimulators-tellurium

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

ecell4-base

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

crn-jax

Chemical reaction networks in JAX: GPU-parallel stochastic simulations.

stochpy

StochPy (Stochastic modeling in Python) provides several stochastic simulation algorithms to simulate (bio)chemical systems of reactions in a stochastic manner.

cbmpy

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

biosimulators-amici

BioSimulators-compliant command-line interface to the AMICI simulation program <https://github.com/AMICI-dev/amici>.