Software

 

AMICI: Advanced Multilanguage Interface to CVODES and IDAS

Python/MATLAB/C++ toolbox for efficient simulation and sensitivity computation for kinetic models

pyPESTO: python Parameter EStimation TOolbox

Python toolbox for the calibration and uncertainty analysis for kinetic models

PETab: PEtab – Specifying Parameter Estimation Problems

Data format for the definition of kinetic model estimation problems

Fides: Reliable Trust Region Optimization in Python

A python implementation of Interior Trust Region Optimization

PySB: Programmatic Rule-Based Modeling in Python

Python toolbox for rule based model formulation