[MOBY-l] lengthy missive on MOBY status after ISMB/I3C

[mwilkinson at gene.pbi.nrc.ca]

Jason Stewart's Response:

mwilkinson at gene.pbi.nrc.ca writes:

> Brian Gilman and I had a serious discussion with them about the
> meaning of "open source", and they appear to be moving in this
> direction.  

Interesting. To me, Open Source is clearly defined. The OSI and their
'Open Source Definition' have seen to that, but yet people can still
get confused. 

Just take for example the ISCB's statement on software:

   The term "open source" has taken on many different meanings. This
   term creates confusion in discussions of software availability;
   therefore the term should be carefully qualified to indicate which
   variation of the open-source model is intended.

No, Open Source has one meaning, as defined by the OSI
definition. However, it does have many *implementations*. And since
those implementations each have different repurcussions it is
important to understand the nuances of the licenses.

> In myGrid, a service-type description includes a designation of the
> input and output for that service type.  In MOBY, inputs and outputs
> are associated with a service *instance* rather than a service
> *type*.

I believe that our way better capture's the task at hand - here's a
data type I've got, what can I do with it? Unless the types are broad,
how are biologist's supposed to understand the nuances between 30
different inter-related BLAST-types? But if they ask for a blast
service, and they have a list to choose from, we should be giving them
a way to learn what output they'll be getting back.

> but what struck me was a related scenario where you send a list of
> objects to a service, and it returns a list of response
> objects... but there is no way to correlate which input object
> resulted in which output object!

What about BLAST? That is built into the output already. You give
multiple query sequences, and you get a list of blast records indexed
by query sequence. So there's no ambiguity. Do you have a case in mind
where the input query is not already part of the output?

jas.