A short CV

Henning Schmidt received a double MSc degree in Electrical Engineering from the TU Darmstadt and SUPELEC in Paris 1997, and a PhD degree in control theory from the Royal Institute of Technology in Stockholm 2004. During his following employment at the Fraunhofer-Chalmers Research Centre in Gothenburg he worked on modeling, simulation, and analysis of biochemical systems and developed the Systems Biology Toolbox for MATLAB (SBTOOLBOX). Currently, he is employed as senior research fellow at the University of Rostock, working on several modeling projects and on a new version of the SBTOOLBOX(2).

Tutorial Abstract

The Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB offers systems biologists a powerful, open, and user extensible environment, in which to build models of biological systems. Experiments can be performed on models, just like in real lab life but in silico. The representation of models, experiments, and measurement data is intuitive and easy to use. The toolbox features a wide variety of analysis tools for biological systems and MATLAB adds to that by a large number of inbuilt functions and a high level scripting language, allowing the user to quickly and efficiently add new functionality.
The SBPD extension package (SBPD) for the Systems Biology Toolbox 2 adds high-speed simulations, combination of models, experiments, and measurement data in so called projects. Functions are available that support the complete model building process (modeling, simulation, identifiability analysis, model reduction, parameter estimation [multiple experiment and multiple measurement fitting], validation, etc.). The projects are a powerful construct that allows keeping a perfect overview over your modeling tasks at any time. Graphical user interfaces support the workflow and give even MATLAB inexperienced users access to most of SBPDs functionality.

The Systems Biology Toolbox 2 is free software and can be downloaded at:

www.sbtoolbox2.org

 Proposed Tutorial Outline

•        General introduction to the toolbox

•        Representation of models/experiments/measurement data

                o        Equation based modeling

                o        Modeling based on biochemical reaction equations

                o        Experiment descriptions and merging with models

                o        Excel and CSV measurement representation

 •        Demonstration of the capabilities of the Systems Biology Toolbox

                o        Simulation (stochastic and deterministic), visualization

                o        Steady-state analysis and stability

                o        Mass conservation

                o        Bifurcation analysis

                o        Parameter sensitivity analysis 

                          (steady-state & oscillating systems, local   & global)

 •        Demonstration of the SBPD capabilities

                o        High performance computation via MEX simulation functions

                o        Projects

                o        Parameter estimation / manual tuning /  parameter fit  analysis

                o        Parameter identifiability analysis

                o        Model reduction

The participants of the tutorial are invited to bring their own laptops to get some hands-on experience.  The toolbox requires at least MATLAB R2006a to be installed. Additional material will be made available [link to be announced] a few days before the tutorial begins.