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(Work planned on the specification)
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Certain previously-planned changes for L3 (documented on [[Community/Wiki/SBML_Level_3_Core | this page]]) are being dropped:
Certain previously-planned changes for L3 (documented on [[Community/Wiki/SBML_Level_3_Core | this page]] are being dropped:

Revision as of 09:57, 27 March 2009

This is a page of subprojects in the development of SBML Level 3 Core.

Work planned on the specification

Task Description Lead Person
 :done: Import L2v4 files Do the SVN work necessary to import the files from L2v4 as a starting point for L3 Core. Mike
Describe packaging scheme L3 will have a packaging construct to allow models to indicate which L3 packages are required for interpreting the model. Mike
 :done: Remove SpeciesType and CompartmentType and related attributes and validation rules The SpeciesType and CompartmentType constructs will be removed in L3 core; packages that need them will provide them instead. Frank
Remove default values on optional attributes & make necessary adjustments Default values on optional attributes are being removed in L3. The component definitions need to be changed appropriate, the text needs to be rewritten to account for this, and we need to add explanations of the implications. Stefan
Introduce an IDRef type Currently, the types SId and UnitSId are used as the data type for both the identifier definition and references to those identifiers. L3 Core will introduce SIdRef and UnitSIdRef for the data types of references to identifiers. (This is primarily to make things cleanear for the introduction of XPath-based references in the L3 hierarchical modeling extension.) Stefan
Update the units section Tasks: (1) Explain what "no defaults" means for units; (2) Add avogadro unit (also add a corresponding mathml csymbol); (3) Remove predefined units for length, area, volume, amount, time; (4) Add attributes to model for length, area, volume, amount, extent, time. Stefan
Update the reactions section Tasks: (1) Add new attribute for 'compartment'; (2) Update section about local parameters to introduce a new object type; (3) Update the section about Stoichiometry to (a) explain reaction extent, (b) add sections for stoichiometry and conversion factor and (c) remove stoichiometryMath Sven
Remove the parts of the spec that belong in a Best Practices document Darren
Remove parts of the explanation of kinetics for multicompartment models The current long section about how to encode multicompartmental reactions needs to be moved to a separate best practices document, and expanded to handle issues brought up by Jannie Hofmyer. Sven
Generate new UML diagrams with all the planned changes Mike
Update all the examples Sarah
Update the validation rules Sarah
Write an appendix listing all the changes compared to L2v4 Mike
Update the MathML subset Stefan

Certain previously-planned changes for L3 (documented on this page) are being dropped:

    • add general section about XPATH (including restrictions that apply for all uses of XPATH in SBML)
    • check all places where we so far used IDs to reference SBML objects.
  • The 'outside' compartment will not be deprecated after all

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