Bioperl: Same random thoughts on the OMG responses

Georg Fuellen fuellen@dali.Mathematik.Uni-Bielefeld.DE
Thu, 13 Nov 1997 11:38:39 +0000 (GMT)

Just a few very casual notes on the various OMG RFI responses...
(currently these are documents  97-11-07 to 97-11-20 at
Corrections/additions are more than welcome. Especially:
   What else is out there, who did not respond to the RFI ?
   Any hints would be very much appreciated !

The EBI response is really worth scrutinizing. It's very comprehensive, incl. 
nice tables.  They seem to be committed to move away from flat files: no 
format conversions, no SRS, etc, etc.
Neverless, flat files will probably be around for a long time, we need to 
tackle the issue now, at least by way of the ReadSeq interface ??!!
EBI's sequence database has a CORBA wrapper prototype... I'm
wondering whether it includes the NCBI taxonomy ?!
(I hope to release a beta of my Bio::Phy object for handling taxonomy/
phylogenetic information early next year - inquiries for the alpha are 

I feel that we should take an in-depth look at EBI's ``AppLab'',
at  **Anyone who could take a
closer look and report back ?**

>From the UCL response, I noted that "CINEMA is written in
Java and works with a Perl/CGI server". **Anyone who could take a 
closer look and report back ?**

The Oxford Molecular Group suggests ``GCG config files'' but
I feel EBI's AppLab may have a better future ?!

GDB ( has OO-schemes "for genes, pcr primers,
clones, and maps". The Roslin Institute has OO-schemes, too
(, as has the Drosophila Genome Center
at Berkeley. 

Sequana also has an object hierarchy and
"is implementing CORBA-based services for approx.
30 different types of nucleotide and sequence analyses."

Tambis (U Manchester) seems to be a very big project indeed, with 
aims well beyond ours.

NetGenetics has some interesting diagrams, w/ many admin objects
like sequence factories, analysis manager, etc, in relation to their
"Synergy" project. Also alignment objects.

The Birkbeck response is concerned with XRay/Electron Microscopy/Molecular
Modelling, and it says ``However, we believe that comprehensive
standard definitions of protein or DNA structures are unlikely to be
successful''. They've done a big C++ library for bioinformatics, we
should ask them about their negative and positive experiences.

best wishes,
Georg Fuellen, fuellen @, fuellen@ nospam
Univ Bielefeld, Research Group in Practical Comp Science   Fax +49 521 106 6411   BioMOO : GeorgF   Fon +49 521 106 2903

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