Sbml Python Packages

cobra

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

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

amici

High-performance sensitivity analysis for large ordinary differential equation models

pysces

The official PySCeS project source code repository.

memote

memote – the genome-scale metabolic model test suite

sme

Spatial bio-chemical reaction model editor and simulator

biomodels

Python library to download and cache models from BioModels

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) Python Package

cbmpy

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

casq

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

biosimulators-tellurium

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

biosimulators-amici

AMICI 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-gillespy2

GillesPy2 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

biosimulators-boolnet

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

efmlrs

Extracts EFMs from result file of mplrs and decompresses EFMs from efmtool and mplrs results that have been compressed with EFMlrs

biosimulators-cbmpy

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

biosimulators-masspy

MASSpy mathematical simulation program via BioSimulators-compliant command-line interface and Docker container

cnapy

An integrated visual environment for metabolic modeling methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!