In biology, a metabolic network describes a set of chemical reactions. The network can be modeled by a bipartite graph with two types of vertices: reactions and substrates. Domain experts wish to reason both about the global network as well as about local networks, subgraphs that are called pathways. Providing a view that combines both aspects is difficult. A first step was made with the MetaViz layout algorithm [1].

The aim of this project is to make several improvements to the visualization of metabolic networks. Because of the way the layout algorithm works, pathways can be either completely preserved, partially preserved, or completely distributed over the network. In the visualization, this is conveyed to some extent by introduction of metanodes that contain a whole or partial pathway. This is not so easy to interpret for the user. It is also hard to understand what exactly it means if there is an edge between two metanodes. Both the visualization of metanodes and edges between them should therefore be improved. Since a pathway may be completely scattered over the network, a user may still want to see that pathway drawn in a familiar way. This might be achieved by two linked views: one that provides a pathway drawing and another that provides a view of the whole network.

[1] Bourqui et al., Metabolic network visualization eliminating node redundance and preserving metabolic pathways, BMC Systems Biology 1:29, 2007.

• Java implementation of the MetaViz layout algorithm
• Improvements to the visualization of the metabolic network
• Coupled view of both whole network as well as pathways