Search Packages

cobra

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

pybel

🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)

biosimulators-utils

Utilities for building standardized command-line interfaces for biosimulation software packages

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

sbmlmath

SBML MathML ↔ SymPy

pybiopax

PyBioPAX: A python implementation of the BioPAX object model

micom

Microbial community modeling based on cobrapy.

napistu

The core library of the Napitsu project supporting the creation, transformation, and network-based interrogation of biological pathways

biosimulators-test-suite

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

ecell4-base

A software platform for modeling, simulation and analysis of complex, heterogeneous and multi-scale systems like the cell. E-Cell has multi-algorithm, multi-timescale and multi-spatial-representation as its central feature.

kisao

Ontology of algorithms for analyzing biological models, their parameters, and their outputs

pypesto

python Parameter EStimation TOolbox

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

pycotools

A Python Toolbox for COPASI

biosimulators-tellurium

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

biomass

A Python Framework for Modeling and Analysis of Signaling Systems

petab-select

Model selection for PEtab

pybel-tools

A PyBEL extension for analyzing BEL graphs

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