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Mark M. Shovman, James Bown (University of Abertay, Dundee, UK)
Link charts (aka network diagrams) are a common visualisation technique, representing abstract connections between entities as glyphs connected by lines. Graph layout, i.e. a position for every glyph and a path for every connection, can be detemined either manually or automatically. Many algorithms for automated graph layout exist, in either 2D or 3D; most of these assume the links to be (a) binary and (b) uniform in their semantics. SBML (Systems Biology Markup Language) describes biological networks in terms of species and reactions, which lends itself well to visualisation as a link chart; but most of the reactions are at least ternary, and have varying semantics (e.g. a reaction where one species breaks down into several, as opposed to a reaction where one species serves as an inhibitor to the transition of a species into another one). We present an algorithm of automated 3D layout of SBML networks, based on the spring-force metaphor, and adapted for n-ary links and distinct link semantics.