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SBML Level 3 Package: Layout ('layout')

Guages, Ralph and Rost, Ursula and Sahle, Sven and Wengler, Katja and Bergmann, Frank T. (2013) SBML Level 3 Package: Layout ('layout'). SBML Level 3 Package: Layout ('layout'), V1 Release1. .

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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.

Item Type:Report or Paper (Documentation)
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Series Name:SBML Level 3 Package: Layout ('layout')
Issue or Number:V1 Release1
Record Number:CaltechAUTHORS:20141028-151228806
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:50957
Deposited By: Linda Taddeo
Deposited On:03 Nov 2014 21:47
Last Modified:03 Oct 2019 07:28

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