Distributed Simulation and Information Visualization Tools for Metabolic Engineering

The main purpose of metabolic engineering is the modification of biological systems towards specific goals using genetic manipulations. For this purpose, models are built that describe the stationary and dynamic behaviour of metabolic networks, i.e. biochemical reaction networks of the cell. Based on these models, simulations are carried out with the intention to understand the cell's behaviour.

However, an enormous amount of data is generated during these simulations, which makes their manual interpretation almost impossible. For this reason, visualization techniques that help to explore this data are needed. Our work in this direction is divided into several tracks:

Visualization and animation of metabolic networks based on data generated during simulations.
Our work is concerned with developing techniques for automatically animating the timely evolution of a metabolic network beyond static snapshots of the simulated data. Furthermore, 2D and 3D visualization techniques for metabolic networks and adaptations of graph drawing algorithms (by including biological know-how) to automate as much as possible the task of graphically designing metabolic networks are investigated.
Visualization of time-varying sensitivity matrices.
Sensitivity analysis is a special tool used in simulation to analyze the sensitivity of a model with respect to its parameters. The results of sensitivity analysis are large time-varying matrices, which need to be properly visualized. However, the visualization of time-varying high-dimensional data is a challenging problem. The methods currently investigated by us are:

(a) tabular visualization methods, such as Reorderable Matrices
(b) projection (or dimension reduction) methods such as Multidimensional Scaling

Since the data sets to be visualized are very large, the possibility of distributed (Grid Computing based) methods for their visualization is currently also being investigated.

Funding: Deutsche Forschungsgemeinschaft (DFG, SPP 1063), 2002 - 2006