Sbml Python Packages

cobra

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

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 Model Editor python bindings

amici

High-performance sensitivity analysis for large ordinary differential equation models

sbmlmath

SBML MathML ↔ SymPy

pysces

The official PySCeS project source code repository.

memote

memote – the genome-scale metabolic model test suite

biosimulators-test-suite

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

metevolsim

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

cbmpy

CBMPy: https://systemsbioinformatics.github.io/cbmpy/ is a platform for constraint based modelling. It implements popular FBA analyses, model editing and supports the latest SBML3FBC standards.

biosimulators-copasi

COPASI 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-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-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

pyvipr

Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML

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

biomodels

Python library to download and cache models from BioModels

biosimulators-cbmpy

CBMPy 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-masspy

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