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Allyson Lister wrote:

> - about CompartmentType and SpeciesType removed: At the end of the longer
> description, it says "It is expected that a small typing package will be
> developed for Level 3 that models can use to add type/category information."
> I understand the logic that led to you removing these types and I agree. I
> was just wondering about the "it is expected" part of the sentence. While
> many people haven't taken this up yet, it is a good idea in general and a
> typing package would be great. So, is it only expected, or is it pretty sure
> that it will be made?

Hi Allyson,

SpeciesType is a crucial part of the package multi. So whether we provide it in a separate package or not, it will be there.

> - Just a note to say I like the idea of the addition of optional
> compartment to reactions :)

Just a note to say that I am completely depressed by the idea of this addition. I understand the rational, but this will be abused really quickly (software will use this information to set or interpret multi-compartment reactions). And it may not help people to understand the difference between the kinetic law, that is the reaction extent per time, and the change in a species quantity.

> - Finally, I agree with Lucian's points about the clarity of the package
> listings, and about the versioning.

I concur


--
Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
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http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/
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