[Biocorba-l] BSANE and bioCORBA

[Juha Muilu]

Hi
We must really start to work more to get the BSA/BSANE and bioCORBA
threads to merge. It is very unfortunate to have this current situation,
where people have to choose from two incomplete specifications. We
should join our efforts and not put lot of time in reinventing the
wheels. Phew :-)

I have been trying to put pieces together and to make the new BSANE
(spec which will now replace the BSA BioObjects) proposal close to the
bioCORBA. There are some small differences in the models which makes the
merging difficult and leads to unnecessary complications like diamond
inheritance.

One problem is the bioCORBA "three layer" sequence model I wonder how
necessary it is to preserve this model? For example AnonymousSequence is
not used at all in the current bioCORBA.

Would it be possible to drop one of the layers. For example the
PrimarySequence and then have  method get_anonymous_sequence in the Seq
interface. I have understood that the model is because of memory
optimization. The AnonymousSequence is more light weight than the
PrimarySequence so why not use that then... ?

I have been trying to compile some web pages about the possible
solutions. Those are in 
http://industry.ebi.ac.uk/~muilu/OMG/BSANE. 

The main idea is to make simple and independent modules which can be
used without having to implement lot of unnecessary stuff. Current
bioCORBA can form the sequence core and then the biosequences with
alphabets can go to a separate module and so. 

Please have a look and let's talk. I would be happy to join to the
bioCORBA team.


Juha

 
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 |Juha Muilu, Ph.D., EMBL Outstation| Email:  muilu@ebi.ac.uk         |
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