Tag: Dynamical System

Data2Dynamics 170117 – Modeling Environment Tailored to Parameter Estimation in Dynamical System

Data2Dynamics 170117

:: DESCRIPTION

The Data2Dynamics software package is a collection of numerical methods for quantitative dynamic modeling and a comprehensive model and data description language. The software facilitates the construction of dynamical models for biochemical reaction networks, but is not limited to this.

::DEVELOPER

D2D development team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • MatLab

:: DOWNLOAD

 Data2Dynamics

:: MORE INFORMATION

Citation:

Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems.
Raue A, Steiert B, Schelker M, Kreutz C, Maiwald T, Hass H, Vanlier J, T?nsing C, Adlung L, Engesser R, Mader W, Heinemann T, Hasenauer J, Schilling M, H?fer T, Klipp E, Theis F, Klingmüller U, Sch?berl B, Timmer J.
Bioinformatics. 2015 Jul 3. pii: btv405.

PottersWheel 4.0 – MatLab Toolbox of Mathematical Modeling of Dynamical Systems

PottersWheel 4.0

:: DESCRIPTION

PottersWheel is a MATLAB toolbox for mechanistic mathematical modeling. It allows reaction network or ordinary differential equation (ODE) based modeling.

PottersWheel has been developed to provide an intuitive and yet powerful framework for data-based modeling of dynamical systems like biochemical reaction networks. Its key functionality is multi-experiment fitting, where several experimental data sets from different laboratory conditions are fitted simultaneously in order to improve the estimation of unknown model parameters, to check the validity of a given model, and to discriminate competing model hypotheses. New experiments can be designed interactively. Models are either created text based or using a visual model designer. Dynamically generated and compiled C files provide fast simulation and fitting procedures. Each function can either be accessed using a graphical user interface or via command line, allowing for batch processing within custom Matlab scripts.

::DEVELOPER

TIKANIS GmbH

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • MATLAB

:: DOWNLOAD

PottersWheel

:: MORE INFORMATION

Citation

Mathematical modeling of biochemical systems with PottersWheel.
Maiwald T, Eberhardt O, Blumberg J.
Methods Mol Biol. 2012;880:119-38. doi: 10.1007/978-1-61779-833-7_8.