Bioperl: Bioperl at ISMB-98

Steve A. Chervitz
Wed, 6 May 1998 18:53:15 -0700 (PDT)

I want to take this opportunity to let everyone know that there will be a 
Bioperl poster at this years ISMB meeting in Montreal, June 28 - July 1:
  (ISMB = "Intelligent Systems For Molecular Biology")

See our abstract below. We are also planning to hold an informal Bioperl  
discussion for all interested parties at the meeting, most likely on the 
29th during/after the poster session. It would be nice to have a critical 
mass of Bioperlers at the meeting. Early registration ends on May 23.

Some items to discuss at the meeting:

 -- What modules are people working on? (Status report)
 -- What modules should we be working on?
 -- Opinions about the recently proposed NCBI toolkit interface.
 -- Relation to other programming languages: what are people using 
    besides Perl?; how does Perl help/hinder development?
 -- Is there enough interest in a separate Bioperl conference?
If anyone has additional suggestions along these lines, please feel free 
to post them to this list.


Steve Chervitz
Department of Genetics         
Stanford University


Bioperl: Standard Perl Modules for Bioinformatics 

The Bioperl project is a coordinated effort to collect computational 
methods routinely used in bioinformatics into a set of standard, 
well-documented, and freely available Perl modules. Perl 
provides unparalleled support for many tasks common in bioinformatics yet 
there are no standard Perl modules for biology. In this poster, we present 
the core modules being designed for key entities in computational
biology: sequences, sequence alignments, three-dimensional molecular 
structures, and sequence comparisons such as BLAST. Also presented is a 
set of integrated modules for genomic analysis which models the essential 
features and interrelationships of biological objects. The Bioperl 
project is open to all and we invite suggestions and participation from 
the bioinformatics community. The Bioperl homepage can be found at:

S. A. Chervitz(a), G. Fuellen(b), C. Dagdigian(c). and S. E. Brenner(d)

(a) Department of Genetics, Stanford University, Stanford, CA 94305-5120 
(USA), Fax 650 723 7016, email:

(b) Universitaet Bielefeld, Techfak - AG PI, Postfach 100131, D-33501 
Bielefeld (Germany), Fax +49 521 106 6411, email:

(c) Genetics Institute, 35 CambridgePark Dr., Cambridge, MA 02140 (USA).

(d) Department of Structural Biology, Stanford University, Stanford, 
CA 94305-5400 (USA).

Perl, standardization, object-oriented programming, freeware, biological 
sequence, alignment, BLAST, protein structure, genomic analysis, Unified 
Modeling Language. 

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