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Workplan

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

Work planned on the specification

Task Description Lead Person
Image:Done.gif Import L2v4 files Do the SVN work necessary to import the files from L2v4 as a starting point for L3 Core. Mike
Image:Done.gif Describe packaging scheme L3 will have a packaging construct to allow models to indicate which L3 packages are required for interpreting the model. Mike
Image:Done.gif 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
mostly Image:Done.gif 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. Frank
Image:Done.gif 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.) Frank
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. Additional changes: stoichiometry is optional. Sven
possibly Image:Done.gif Remove the parts of the spec that belong in a Best Practices document Darren, Mike, Sarah, Frank
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
Image:Done.gif Generate new UML diagrams with all the planned changes Mike
Image:Done.gif Update all the examples Sarah
Update the validation rules Sarah
Write a companion document documenting all the changes compared to L2 Mike
Image:Done.gif Update the MathML subset Sarah
Image:Done.gif Remove "outside" on compartment It looks like we're removing it after all. The section on compartments needs to be updated. Frank
Image:Done.gif Remove "charge" on species It's been deprecated and planned for removal.
Image:Done.gif Clarification about effects of compartment size changes on species The Level 2 spec does not explain what happens to concentration/amounts of species when compartment sizes change. It should say what's fixed is the amount. Sven, Frank, Mike
Image:Done.gif Remove restriction on zero-length listOfs In the list of event assignments (in an Event) and list of units (in a UnitDefinition), the lists are stipulated as having to have at least length 1. This restriction is being removed. Mike (diagrams)
Image:Done.gif Best practice explanation about algebraic rules & events Sarah
Image:Done.gif Remove duplication of info about allowable sboTerm attribute values Descriptions of sboTerm values should appear only in one place, in the section on SBO. The individual definitions of the sboTerm attribute should point to the section instead of trying to summarize what the allowed vocabularies are for each SBML component. Frank
Develop new XML Schema The new XML Schema has to have changes for the other parts of Level 3, and also for removing restrictions on element ordering Stefan, Mike
Image:Done.gif (except for compartment unit section) Remove restrictions on spatialDimensions Restrictions on Compartment sizes will be removed Frank
Statements about default values may be best practices now Check that previous L2v4 statements about assumptions about default values are maybe mentioned as best practices, if appropriate
Add sbml:units to MathML cn
Verify that section on SBO is up to date
Verify that section on annotations is up to date


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

  • XPATH
    • 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.

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This page was last modified 02:53, 5 August 2009.



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