[MOBY-l] (ping Lincoln) caBIO... can we start a brief discussion of this project

[mwilkinson at gene.pbi.nrc.ca]

Hi all,

I'm getting near the end of the BIB manuscript on BioMOBY, and am at the
point where I am discussing MOBY v.v. other integration projects,
comparing the similarities/differences.

I'm quite stuck on caBIO... not because I can't find information about
it, but because I am having trouble understanding what the real benifits
are of their approach.  The most significant difference in the two
projects seems to be that MOBY objects are (at the moment) data-only,
while their objects have methods.  The inclusion of methods seems to me
to lead to the onerous responsibility of re-creating BioPerl or BioJava
over SOAP...

I agree that it is nice w.r.t. client design if you simply have an API
that "just works"... but on the other hand, when writing Genquire we
found that the BioPerl API wasn't always powerful enough for us, and we
had to build additional methods into our  inherited modules.  I don't
think it is wise to anticipate a priori what a client is going to want
to do with the data...

Also, unless I am mis-understanding the situation, there seems to be an
undesirable degree of centralization involved in their architecture.
The objects have to be created somewhere, and not all data is available
at one place, so there is some sort of "proxy"?  that collects the
required data and passes it to the client...??  Is that right?

Lincoln, I am assuming that you know more about the project than I do,
as you invited the two caBIO representatives to the last MOBY meeting.
Can you clarify any of these issues for me?  Or anyone else who is "in
the know" and has used caBIO before?

Any advice is appreciated!

Mark


--
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"Speed is subsittute fo accurancy."
________________________________

Dr. Mark Wilkinson, RA Bioinformatics
National Research Council, Plant Biotechnology Institute
110 Gymnasium Place, Saskatoon, SK, Canada

phone : (306) 975 5279
pager : (306) 934 2322
mobile: markw_mobile at illuminae.com