Sbml Python Packages

cobra

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

petab

Python package for working with PEtab files

sbmlmath

SBML MathML ↔ SymPy

sbmlutils

Python utilities for SBML

amici

High-performance sensitivity analysis for large ordinary differential equation models

sbml2cellml

SBML ↔ CellML converter

sbml4humans

SBML4Humans: SBML report for humans

sbmlsim

sbmlsim: SBML simulation made easy

pysces

The official PySCeS project source code repository.

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.

biomodels

Python library to download and cache models from BioModels

axiomize

Reproducible scientific modeling engine and agent skill pack: versioned Model IR with mandatory units, dimensional and numerical validation, calibration, uncertainty analysis, and portable export (SBML, CellML, Modelica) via CLI, REST and MCP. Install: pip install axiomize.

memote

memote – the genome-scale metabolic model test suite

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

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.

cbmpy

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

biosimulators-tellurium

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

casq

CaSQ: Celldesigner as Sbml-Qual [https://gitlab.inria.fr/soliman/casq/ mirror]

biosimulators-amici

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

biosimulators-gillespy2

GillesPy2 biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

biosimulators-pysces

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

biosimulators-cobrapy

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