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Visualization of complex biochemical models with ProMoT


Mirschel,  S.
Systems Biology, Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society;

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Mirschel, S. (2009). Visualization of complex biochemical models with ProMoT. Talk presented at Waterman Seminar Series on Bioinformatics. Gatersleben, Germany. 2009-08-12 - 2009-08-12.

In recent years modeling of reaction systems tend to be more complex. Especially in systems biology researchers are faced with large and highly interconnected network models that become hard to understand and navigate. The hierarchical decomposition of models into modules and the consequent graphical representation of these units can help to understand complex models and make them more manageable. However, in terms of visualization, this approach has some limitations due to the size and complexity of models and the lack of screen real estate. In this talk, visualization and navigation techniques for complex biochemical network models are introduced. They provide basically two functionalities - (i) the interactive visual exploration of model parts in context of the whole model and (ii) a highly flexible handling of visual properties of the network model tailored to user preferences and the modeling task. The techniques are illustrated by applying them to different application areas including chemical engineering and systems biology but with focus on intracellular reaction systems such as signaling networks. Furthermore, it is discussed how these techniques are used for the adequate visual representation of the logical/Boolean modeling formalism and for the visualization of data derived from model analysis. This talk also presents a first approach for the semi-automatic layout of models with hierarchical and modular structure. The techniques are implemented in the process modeling tool ProMoT (