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Layout

SBML Level 3 Package Activity Status Page

Package objectives

Many software systems for modeling allow a user to create and interact with the model in the form of a reaction graph. However, SBML Level 2 does not define a format for storing these graphs in a model, which means that the information about how the user organized and drew the graph is lost when the model is exchanged between software tools. A given tool may add annotations to the SBML to make it possible to recover the layout, but another tool will not be able to use it unless both tools agree about the format of the annotations. The diagram layout package refers to a proper standard for including model diagrams in SBML.

The short label for this package is layout.

Active proposals

The SBML Development Process for SBML Level 3 defines two stages: a proposal stage, and a specification development stage. Nearly all SBML Level 3 activities are currently in the proposal stage. The exception is the layout proposal, for which a de facto proposal has been accepted. SBML Level 3 Layout is now in the specification development stage (see next section).

www.copasi.org COPASI] group have volunteered to lead the layout effort and have made tremendous progress. Their approach separates layout from rendering. The latter defines the graphical representations, or glyphs, of different SBML model elements such as compartments, species, and reactions, and the former provides information about where to place the glyphs on a screen or on paper. By broad consensus in the SBML community, the Gauges et al. layout package proposal is now the de facto approach in the SBML community. Several groups besides the COPASI project either already support it or have indicate they would support it.//www.copasi.org COPASI] group have volunteered to lead the layout effort and have made tremendous progress. Their approach separates layout from rendering. The latter defines the graphical representations, or glyphs, of different SBML model elements such as compartments, species, and reactions, and the former provides information about where to place the glyphs on a screen or on paper. By broad consensus in the SBML community, the Gauges et al. layout package proposal is now the de facto approach in the SBML community. Several groups besides the COPASI project either already support it or have indicate they would support it.

Active specifications

The layout activity area for SBML Level 3 is currently in the specification development stage. A provisional definition for SBML layout has been produced by Gauges et al. and has been in use for a few years.

projects.villa-bosch.de/bcb/sbml/ Link to layout pages by Gauges et al.]//projects.villa-bosch.de/bcb/sbml/ Link to layout pages by Gauges et al.]

Until a specification for SBML Level 3 is released, the provisional way of using the layout extension is by storing the layout data (defined in the provisional specification) inside SBML annotation elements in a model. When Level 3 becomes available, the layout can simply be moved out of the annotation block on individual SBML elements and onto the elements themselves.



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