[Biojava-l] ResidueList & Annotatable

[Matthew Pocock]

Dear Biojavaerers,

Ewan and I have talked face-to-face. The upshot is that we shall move our current
sanger biojava code base under the biojava cvs server. I will post details of how
to access this & edit/contribute code as soon as I can.

This first set of code is meant as a starting point. It has worked for us, but may
be inappropriate for wider use, so if you spot bugs/oversights or just plain
stupidness, this is the mailing list to discuss it, and CVS is available to change
it.

I know that many of you have written similar software and libraries. Biojava
should grow into the first stop resource for biological problem solving in Java,
so tell us what we are missing and get it included. There will be room for
programs as well as library code - ranging from simple tutorial examples through
to fully fledged useful programs.

I am happy to take responsibility for making sure that the list and the code base
hang together. However, this is a temporary and unendorsed position, so as time
goes by a more natural choice of leadership will probably emerge.

We shall initially put everything under LGPL
(http://www.gnu.org/copyleft/lesser.html). I have personal views about licensing
and credit for coding, but I am sure that you all do as well. Licenses can always
be changed by agreement, and we can license different bits of the code base
differently if that is what is appropriate.

I look forward to all of us coding together.

Matthew

Matthew Pocock wrote:

> Hi Ewan.
>
> Thanks for the mail. I don't know if I am the best person for managing
> anything, but I can at least get the ball roling over the next 2-3 months and
> then drop out if somebody obvious is available.
>
> Ewan Birney wrote:
>
> > 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.
>
> I totaly see your CORBA point - I would not like to be responsible for writing
> an IDL with an object/residue implementation of a sequence - not with
> objectOnServer corba (mabey with the corba where objects can migrate...).
>
> >
> >
> > 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 think that it would be a good thing to write a standard bridge from biojava
> to a suitable biological IDL, but the java doesn't have to look identical in
> every way in java-land.
>
> >
> > I would really like to encourage you Matt to take the lead on
> > biojava and do two things
> >
> > a) Coordinate the list/code
>
> Sounds scary.
>
> >
> >
> > b) Get the code under cvs in some public place.
>
> This one is close to my heart. When can I come over to see you?
>
> > First thing - cvs code base. We can set it up now if you like ;).
>
> Grab me when you get back from lunch.
>
> >
> >
> > -----------------------------------------------------------------
> > Ewan Birney. Mobile: +44 (0)7970 151230
> > <birney@ebi.ac.uk>
> > -----------------------------------------------------------------
> >
> > _______________________________________________
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