Search 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.

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

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.

metevolsim

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

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-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

pyvipr

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

biosimulators-boolnet

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

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

biomodels

Python library to download and cache models from BioModels

yaml2sbml

A small package to convert ODEs specified in a YAML file to SBML/PEtab