Workplan

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

Work planned on the specification

	Task	Description	Lead Person
	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
	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	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
	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	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
	Generate new UML diagrams with all the planned changes		Mike
	Update all the examples		Sarah
	Update the validation rules		Sarah
	Write a companion document documenting all the changes compared to L2		Mike
	Update the MathML subset		Sarah
	Remove "outside" on compartment	It looks like we're removing it after all. The section on compartments needs to be updated.	Frank
	Remove "charge" on species	It's been deprecated and planned for removal.
	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
	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)
	Best practice explanation about algebraic rules & events		Sarah
	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
(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.