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Hi Allyson,

AL> - about CompartmentType and SpeciesType [...]
AL> while many people haven't taken this up yet, it is a
AL> good idea in general and a typing package would be
AL> great. So, is it only expected, or is it pretty sure
AL> that it will be made?

I'd personally like to see it definitely done. I think a
simple scheme would be easy enough to define and introduce.
The strawman proposal I had in mind is a list of types with
basically no attributes except the standard id & name,

<listOfTypes>
<type id="someSpeciesType1">
<type id="someSpeciesType2">
<type id="someCompartmentType1">
<type id="someCompartmentType2">
<type id="someCompartmentType3">
</listOfTypes>

coupled with an optional attribute on every component to
indicate the component instance belongs to a type:

<listOfCompartments>
<compartment id="C1" ...>
<compartment id="C2" type="someCompartmentType1" ...>
<compartment id="C3" type="someCompartmentType2" ...>
<compartment id="C4" type="someCompartmentType2" ...>
<compartment id="C5" type="someCompartmentType3" ...>
...
</listOfCompartments>
<listOfSpecies>
<species id="S1" type="someSpeciesType1" ...>
<species id="S2" type="someSpeciesType1" ...>
<species id="S3" type="someSpeciesType2" ...>
<species id="S4" type="someSpeciesType2" ...>
<species id="S5" ...>
<species id="S6" ...>
...
<listOfSpecies>

This would also allow reactions to have reaction types,
parameters to have parameter types, etc. It could hopefully
also serve as a substrate for other packages that need
typing. For example, although nobody's had a chance to
discuss or examine the idea, one could imagine the Multi*
package using this.

Some details still need to be worked out. For example,
types would have mathematical implications for a model. It
would at minimum have to have the same mathematical impact
as the SpeciesType construct in the current L2. (Example: a
compartment can't contain two different species of the same
SpeciesType.)

MH

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