The visualization of metabolic networks using techniques of graph drawing has recently become an important research area. In order to ease the analysis of these networks, readable layouts are required in which certain known network components are easily recognizable. In general, the topology of the drawings produced by traditional graph drawing algorithms does not reflect the biologists' expert knowledge on particular substructures of the underlying network. To deal with this problem we present a constrained planarization method---an algorithm which computes a graph layout in the plane preserving the predefined shape for the specified substructures while minimizing the overall number of edge-crossings
