[Biojava-l] Open source, standards etc.

[Ewan Birney]

On Sun, 23 Jan 2000, Thomas Down wrote:

> > As regards standards, it is probably worth looking at the OMG biomolecular
> > sequence analysis IDL and aiming to make biojava effectively an open
> > source implementation of that. In any case ensuring that the OMG
> > interfaces are included in biojava would IMHO be a Good Thing (tm) I
> > haven't had time to build anyhting yet as the standards were still in
> > development last time I was doing stuff in Java. (then a change of job
> > etc. etc.. but I have a new postdoc who might pick up the ball and run
> > with it.)
> 
> The OMG interfaces are interesting, for sure.  But personally
> I'm not entirely sure I like the way they are based on the
> sequence == (string + annotations).  Take a look at the concept
> of a sequence as implemented in the Sanger Centre biojava core:
> 
>   http://www.sanger.ac.uk/Users/td2/biojava_core_20000121/
> 

I'd actually caution slavish adherence to the OMG standard (and I was one 
of the people who wrote the standard!). It uses too much CORBA 2.2, I'm
not a big fan of their location stuff (Matt's is nicer).

I'd like to see biojava take on interfaces which I am proposing for
bioperl. I am going to be using these interfaces to write a bridge to
the OMG standard from bioperl. If biojava and bioperl can agree on 
a standard set of interfaces then that is good news. I will package up
the interfaces for your perusal soon. I suspect that the best thing is
to get Tom and Matt in the same room and discuss it there.

Tom - I appreciate that your residuelists provide a very nice compute
arena for sequences, but for many, many uses, strings are an *excellent*
way of representing biological sequences and so in-grained into
bioinformatics that I don't see a good argument to give them up. This is
the sort of argument best done in a room however, with Matt.



> It ought to be possible to use our own interfaces in the core
> but add a bridge to the OMG interfaces, if that looks like the
> best way to go.
> 
> Any views on this?
> 
> Thomas.
> -- 
> ``Science is magic that works''  -- Kurt Vonnegut.
> 
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