Perl Conference Handout

[Georg Fuellen]

Hi SteveB,
> Georg,
> 
>   No time to edit the homepage before my return in early Oct.  Feel free
> to steal the text yourself though.  (Note that my text was stolen from the
> homepage and then slighly altered.) 

Can you send me the final version ? (I remember SteveC suggested corrections,
etc)

>   Sorry :(
> 
>   But I will *try* to get UnivAln packaged, with SteveC, so we both learn. 

Actually, Bio::PreSeq needs to be packaged, too, doesn't it ?
(i.e. I think it requires manual editing, too.)

> Where's the version I should pack up? 

http://www.TechFak.Uni-Bielefeld.DE/techfak/persons/fuellen/UnivAln.tar.gz
Note that revcom(), etc, return a subalignment as a string or array, 
and if that's not what we want (from recent discussion, 
I infer that an object needs to be returned), 
this needs to be flagged as ``SUBJECT TO CHANGE'' in all the utility functions.
At least a ``GENERAL REMARK'' is needed.
Are there other prospective changes to the UnivAln interface that should be
marked ?

> Steve
> 
> On Fri, 8 Aug 1997, Georg Fuellen wrote:
> 
> > Just two comments
> > 
> > > My handout for the Perl conferenc will consist of 3 pages.  The first is
> > > the abstract written by Tim O'Reilly and myself, followed by homepage and
> > > mailing list information; the second is the OiB abstract.  The third is a
> > > description of current modules, as below. 
> > > 
> > > I need to mail this by around 10am tomorrow.  If you have any comments,
> > > make sure they get to me before then!
> > > 
> > > 
> > > 
> > > ---
> > > 
> > > Active Bioperl Projects
> > > 
> > > Bio::PreSeq
> > > A Perl module for reading, accessing, manipulating, and analyzing single
> > > biological sequences. 
> > > 
> > > Goal: Provide a standard representation for biological sequences, so that
> > > the same sequence may be submitted to a large number of different
> > > manipulation and analysis functions.
> > > Status: Beta code, Version 0.035 from 26 May 1997
> > > Planed Enhancements: Increased, consistency, error-checking, and more
> > > analysis functions.  Bio::PreSeq is a tentative version of Bio::Seq, and
> > > will be renamed once the interfaces are fully fixed.  Users may build code
> > > on Bio::PreSeq with the knowledge that its interface will remain
> > > reasonably constant, as major changes will be reserved for Bio::Seq.
> > 
> > 1 To the reader this may imply that Bio::PreSeq will be maintained
> > once Bio::Seq is released -- very unrealistic !
> > 
> > 2 It may be the easiest if you edit the current homepage based on this ??
> > (and point me to the HTML so that I can upload it?)
> > 
> > > Chief Developer: Chris Dagdigian, cdagdigian@genetics.com
> > > 
> > > 
> > > Bio::UnivAln
> > > A Perl module for reading, parsing, writing, slicing, and manipulating
> > > multiple biosequences 
> > > 
> > > Goal: Manage and manipulate multiple sequences and their alignments
> > > Status: beta code, Version 1.005 from 18 Jun 97. 
> > > Special features: Flexible slicing, mapping, consensus, (in)variable
> > > sites, gap-free sites, reverse, complement, and reverse complement. 
> > > Planned enhancements: More CGI and Graphics; improved format handling;
> > > better validity checking
> > > Chief Developer: Georg Fuellen, fuellen@Techfak.Uni-Bielefeld.DE
> > 
> > ok
> > 
> > > Bio::Struct
> > > A Perl module for reading, writing, accessing, manipulating, and analyzing
> > > biological macromolecular structures.
> > > 
> > > Goal: Provide a standard and convenient representation for biological
> > > structures, as well as core data-management and analysis features
> > > Status: Conceptual
> > > 
> > > 
> > > Bio::Object
> > > A rich hierarchy which attempts to encode the underlying logic of
> > > molecular biology within a set of standard, interoperable Perl modules.
> > > 
> > > Goal: Provide a framework to help guide the design of interoperable Perl
> > > classes for managing and processing molecular biological data.
> > > Status: Ongoing evolution; currently usable
> > > Special features: Extensively used as part of the SGD database
> > > Chief Developer: Stephen A. Chervitz sac@genome.stanford.edu
> > > 
> > > 
> > > 
> > 
> > 
>