POEM

Parameter Optimisation and Estimation Methods

Description

The goal of this project is to provide comprehensive and flexible software packages for parameter estimation in systems biology, chemical reaction dynamics, nonlinear mechanics, and other fields. Special emphasis is put on an easy-to-use graphical user interface (GUI) and state-of-the-art numerical methods to solve highly nonlinear and ill-posed inverse problems.

The software BioPARKIN has especially been designed for modeling, parameter identification and simulation in systems biology. The GUI uses an intuitive network editor and adheres to system biology standards such as the SBML file format. The underlying numerical framework uses affine invariances and adaptive algorithms as given in [P. Deuflhard, Newton Methods, Springer, 2004].

The package will be available as source code in Python (GUI part) and C++ (numerical part).

Further information is available in the detailed project description. 

Members

Thomas Dierkes

Mascha Berg

Susanna Röblitz

Peter Deuflhard

Former members

Moritz Wade

Uli Nowak

Responsible

Susanna Röblitz