Perl Conference Handout

[Steven E. Brenner]

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!



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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.
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


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