Visualising Metabolic Pathways and Networks: Past, Present, Future

Design considerations for representing systems biology information with the Systems Biology Graphical Notation

“…Even though common graph drawing algorithms can be employed for laying out biological networks in general and SBGN maps in particular, domain specific layout methods that conform to representational conventions in biology as well as special approaches have been developed, and there is a large body of literature available, examples include algorithms for specific biological networks such as metabolic networks [ 9 , 50 ], [ 51 ], [ 52 ], [ 53 ] and protein interaction networks [ 54 ], [ 55 ], [ 56 ], [ 57 ], for general biological networks [ 58 ], [ 59 ], [ 60 ], [ 61 ], [ 62 ], [ 63 ], [ 64 ], [ 65 ], [ 66 ], for 2.5D layouts [ 67 , 68 ] and 3D layouts [ 69 ], [ 70 ], [ 71 ], [ 72 ], [ 73 ], [ 74 ] as well as for specific optimisations or comparisons within the layout [ 75 ], [ 76 ], [ 77 ]. Also open graph drawing problems have been discussed [ 78 ].…”