Bioperl: Re: New Bio::Seq and Bio::Seq::Parse (.025 BETA)

Georg Fuellen fuellen@dali.Mathematik.Uni-Bielefeld.DE
Fri, 18 Apr 1997 12:11:16 +0000 (GMT)

Steve: I agree w/ releasing "Bio::PreSeq" as you suggested below.
Chris - How about you ? Any progress ? (Just pushing you a little bit ;-)

Lew: Regarding CORBA, I feel this is a long-term issue,
and I've asked the poster of the following message whether he's got any 
private responses (there were no public ones it seems). Will forward.

Subject:      CORBA for perl?
From: (David Tauzell)
Date:         1997/04/13
Message-Id:   <5irq6m$>
Newsgroups:   comp.lang.perl.misc
[More Headers]

Does anybody  have any interest in writing a CORBA ORB for
Perl, or has anybody seen one?  The reason I think that this
would be usefull is that several web servers are going to
be using CORBA and IIOP as a replacement for CGI (something like FASTcgi).

It would be nice for Perl to fit within this realm, too.
David Tauzell.  I like unix.

> Georg Fuellen wrote:
> > I agree w/ all the comments you made, and I hope you'll respond to the other
> > issues in a week..
> Glad to hear that we're (at last) in agreement.
> During my trip, I gave some thought to the future developments needed
> by the Bio::Seq module.  I think that it is a great piece of code, though
> it has a few rough spots, especially:
>   * consistency/validity
>   * alphabet support
>   * parsing
>   * numeration
> All of these are implemented, but not necessarily in a way which is
> extensible or efficient.  Since these affect the interface, I think we
> can't release the module as-is.
> On the other hand, correctly rewritting the code for all these features
> could take a long time.  Since the code is certainly usable and important
> as it is, I think that there is great value in just getting it to the
> community. 
> Therefore, I suggest that we release the module as "Bio::PreSeq".  By
> analagy with what's being done with Bio::UnivAln, we will release and
> support Bio::PreSeq for the community.  However, as we better figure out
> how to construct the interface, especially to deal with the items
> mentioned above (and possibly to incorporate other issues), changes to the
> interface will be rolled into a Bio::Seq.
> Do people think this is a good idea?