With the development of the Systems Biology Markup Language (SBML), there now is a common standard for the exchange of dynamical models in systems biology. It has already been adopted by many applications in this field (Hucka et al., 2011, 2003; SBML Team, 2012).
In 2002, we worked on an automatic layout algorithm (Wegner and Kummer, 2005). This algorithm was based on the principle that, given an SBML file, the species and reactions should be placed automatically as a network. Since there was no way to save the final layout of the network, we started developing a layout extension for SBML. In 2003, the first draft was completed and presented at the SBML workshop in St. Louis in 2004. Based on the discussions in St. Louis, Ralph Gauges finalized a first specification and implementation for libSBML (Gauges et al., 2006). During the next several SBML meetings, the layout extension was discussed in depth and also challenged by other proposals, but due to the constant support from the community (e.g., Deckard et al., 2006), it was finally accepted as a package for SBML Level 3
