A graphical tool for visualization of functional modules in biochemical networks

The growing knowledge of biochemical networks leads to more and more complex data and models. Data analysis involves exhausting computation with complex data interpretation. Here, new tools are required for fast and simple analysis. Such tools should provide a graphical visualization of the network and its analysis. Although there exists a number of tools to analyze biochemical networks, visualization tools to represent complex relationships are still lacking.

We present a new tool for the analysis of biochemical networks based on Petri nets. The main focus of the tool is the computation and visualization of functional modules and their analysis. These functional modules are based on Petri net's T-invariants, which can be interpreted as biologically meaningful functional modules. For further decomposition we involved concepts of MCT-sets and T-clusters. Knockout analyses can easily be performed. We support several network formats such as SBML, KEGG, or PNT. The visualization creates a layout of the network, which can be edited and saved in different ways. Color, size, shape, text and style of all network components are fully accessible according to the needs and wishes of the user. To support the visual inspection of the results, functional modules can be highlighted in different colors. All results can be exported as text files in standard formats in order to provide an interface to other tools.

The tool is mainly used for exploring metabolic pathways and signal transduction pathways.