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 bio-chemical reaction model editor and simulator

amici

High-performance sensitivity analysis for large ordinary differential equation models

sbmlmath

SBML MathML ↔ SymPy

biosimulators-test-suite

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

pysces

The official PySCeS project source code repository.

memote

memote – the genome-scale metabolic model test suite

metevolsim

MetEvolSim (Metabolome Evolution Simulator) Python Package

biosimulators-copasi

BioSimulators-compliant command-line interface to the COPASI simulation program <http://copasi.org>.

casq

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

biosimulators-tellurium

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

biomodels

Python library to download and cache models from BioModels

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>.

biosimulators-gillespy2

BioSimulators-compliant command-line interface to the GillesPy2 simulation program.

biosimulators-pysces

BioSimulators-compliant command-line interface to the PySCeS simulation program <http://pysces.sourceforge.net/>.

biosimulators-cobrapy

BioSimulators-compliant command-line interface to the COBRApy simulation program <https://opencobra.github.io/cobrapy/>.

biosimulators-boolnet

BioSimulators-compliant command-line interface to the BoolNet simulation program.

pyvipr

Widget to visualize PySB models in Jupyter Notebook

biosimulators-cbmpy

BioSimulators-compliant command-line interface to the CBMPy simulation program <http://cbmpy.sourceforge.net/>.

biosimulators-masspy

BioSimulators-compliant command-line interface to the MassPY simulation program <https://masspy.readthedocs.io/>.

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!