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Simulator Graphviz
Chaitanya Talnikar edited this page Dec 31, 2012
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The simplest solution.
Server get's the network (jSBGN format), inputs it to graphviz, which in turn makes a nice, already layouted SVG, that is returned to the simulator.
The simulator loads it as a dynamic SVG (no static image include).
Actually the SVG is slightly modified by the server before being returned, in order to allow the simulator node recognition for dynamic access.
- all nodes are equal (ellipse shape)
- all edges/arrows are equal: subtrates, catalysts and inhibitors are not differentiated
- reaction nodes are not shown, every reaction can have only one output
Some of these disadvantages could actually be fixed, see also http://www.graphviz.org/doc/info/attrs.html#k:arrowType, but we are currently focussing on integrating the biographer UI, which will offer us SBGN-conform presentation.