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Layout

(Active proposals)
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__NOTOC__
'''SBML Level 3 Package Activity Status Page'''
'''SBML Level 3 Package Activity Status Page'''
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{{ReferToPkgSpecPage | pkg=layout}}
== Package objectives ==
== Package objectives ==
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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.
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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 SBML Level 3 Layout and [[Community/Wiki/SBML_Level_3_Proposals/Rendering | SBML Level 3 Rendering]] packages together are concerned with providing a standard approach for including model diagrams in SBML.
The short label for this package is <tt>layout</tt>.
The short label for this package is <tt>layout</tt>.
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== Active proposals ==
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== Package specifications ==
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{{#icon:Icon-red-right-arrow.jpg}} A [[Documents/Specifications/SBML_Level_3/Packages/Layout_%28layout%29 | separate page]] is dedicated to the specification development activities involving this package.
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A [http://otto.bioquant.uni-heidelberg.de/sbml/ provisional definition for SBML layout] has been produced by Gauges et al. and has been in use for a few years. Until a final specification is released, the provisional way of using the layout extension is being used.
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== Package proposals ==
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The [[Documents/SBML_Development_Process | SBML Development Process for SBML Level&nbsp;3]] defines two stages: a proposal stage, and a specification development stage. All SBML Level&nbsp;3 activities are currently in the proposal stage.
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Members of the [http://www.copasi.org COPASI] group volunteered to lead the layout effort and 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.
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Members of the [http://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 COPASI have indicate they would support it. Until SBML Level&nbsp;3 is officially released, the provisional way of using the layout extension is by storing the data in <code>annotation</code> elements in a model. When Level&nbsp;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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== Package Working Group (PWG) ==
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[http://projects.villa-bosch.de/bcb/sbml/ Link to layout pages by Gauges et al.]
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After a vote by the SBML community to accept the above proposal as something that addresses a valid need and takes a reasonable approach, we formed a working group to help complete the proposal and resolve any implementation issues that might arise. Membership of this group is open to all interested members of the SBML community; all you need to do is sign up for the [https://lists.sourceforge.net/lists/listinfo/sbml-layout sbml-layout mailing list].

Current revision

SBML Level 3 Package Activity Status Page

Please note: This page is for the proposal of this SBML Level 3 package.
Information on this page is likely to be out of date with current developments.
Current development is focused on the specification of this package.
Specification activity is described on a separate 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 SBML Level 3 Layout and SBML Level 3 Rendering packages together are concerned with providing a standard approach for including model diagrams in SBML.

The short label for this package is layout.

Package specifications

A separate page is dedicated to the specification development activities involving this package.

A projects.villa-bosch.de/bcb/sbml/ Link to layout pages by Gauges et al.]//otto.bioquant.uni-heidelberg.de/sbml/ provisional definition for SBML layout] has been produced by Gauges et al. and has been in use for a few years. Until a final specification is released, the provisional way of using the layout extension is being used.

Package proposals

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 COPASI have indicate they would support it. Until SBML Level 3 is officially released, the provisional way of using the layout extension is by storing the data in 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.//www.copasi.org COPASI] group volunteered to lead the layout effort and 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.

Package Working Group (PWG)

After a vote by the SBML community to accept the above proposal as something that addresses a valid need and takes a reasonable approach, we formed a working group to help complete the proposal and resolve any implementation issues that might arise. Membership of this group is open to all interested members of the SBML community; all you need to do is sign up for the sbml-layout mailing list.



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