[MOBY-l] Biomoby and Taverna 1.2

[markw at illuminae.com]

> If noone (except of Heiko Dirk and me) want the collections to be
> changed in the BioMoby API we will have to change the default behaviour
> of Taverna back to the old one!

I think your use-case for wanting the behaviour of collections to change is
unfounded, since it overloads the intended meaning of the Collection element by
putting WAAAAAAY too much semantics in it.  The use case of having sets of
multiple alignments represented as Collections of Collections means that the
inner-most Collection now not only represents a "bag" of things, but a "bag" of
things that **DO** have a close semantic relationship to each other - these are
a set of related sequences, and a set of related sequences **is a useful
Object** in the context of MOBY, could easily trigger the discovery of a
particular set of services that can specifically operate on sets of closely
related sequences (versus sets of unrelated sequences), and therefore should be
given a class of its own (IMO).

Moreover, if we allow collections of collections, we then have a problem of
recursion - collections of collections of collections of collections of
collections....  What a nightmare!

The API change is not a significant one, I agree... and in fact, since people
are already mis-using the messaging format in this way much of the software out
there can already handle the situation... but given that particular use-case, I
think you are losing more semantics than you need to be by refusing to create a
new Object Class.

M