[Biojava-l] ResidueList & Annotatable

[Ewan Birney]

Matt -

Basically I like the current set up with some fiddles. My only
real bitch is that I don't think the residuelist interface is going
to work well in other languages (thinking about making it
an IDL). I really want a "PrimarySeq" (the latest name of the
lightweight sequence in bioperl) interface to have a string
representation of sequences. Having bioperl and biojava share
an IDL representation is "a good thing" and we should work hard
and getting it right.

Thinking more about CORBA IDLs I think they have to be sideways
to interfaces you use anyway (perhaps) - so I think the IDL discussion
can be decoupled from the way you want to make the bio.seq stuff.


I would really like to encourage you Matt to take the lead on
biojava and do two things

a) Coordinate the list/code

b) Get the code under cvs in some public place. 


I don't want to force people here to adhere to Matt's "view" of the world,
but from bioperl we know two things.

a) you need someone who is responsible for coordinating it. This person
has to have a tolerant view of other people's ideas/input (take note matt.
I think you do in any case) and

b) you need to work from a common code base. Trading JARs or tarballs is
nowhere the same as working on one cvs repository.


I'd encourage people on the list to support matt in this and to hassle
matt when he gets off line. Matt has to be responsible for both
coordinating things and crucially listening to other views. Finally Matt
has to know when to step down and let someone else take over.


First thing - cvs code base. We can set it up now if you like ;).



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Ewan Birney. Mobile: +44 (0)7970 151230
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