Additional file 5.

Integrated Map of Macrophage Pathways in 3D-or-2D View. The integrated macrophage pathway can be viewed in the network visualisation tool BioLayout Express3D, in both 2 and 3-dimentions and also using the original graph co-ordinates as the .graphml file. By choosing the appropriate class-type (found within class tab of graph properties box) the nodes can be coloured according to assigned classes. By default nodes are coloured and shaped according to "node-type" (e.g. proteins, genes, complexes, process nodes) using a 3D-notation scheme described at webcite. Nodes may also be coloured according to sub-cellular location by assigning the "Cellular location" class. It is also possible to import other class-sets of interest; for example information about a components regulation/behaviour in a dataset. Within BioLayout Express3D one can easily follow the flow of information through the pathway by selecting parent or children nodes of a component of interest to highlight them. BioLayout Express3D software is freely available and can be downloaded at webcite

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Raza et al. BMC Systems Biology 2010 4:63   doi:10.1186/1752-0509-4-63