Welcome to the Bioperl Project !

      What's New (December 9, 1998):
      New release of the Bioperl modules --
      Please visit our new homepage.
      This site is now relevant only as the distribution site for
      any upcoming standalone versions of the UnivAln.pm module,
      and for people interested in history.
      What's New (August 18, 1998): Our new Homepage, bio.perl.org.

      • Introduction
      • Current core modules
        • Bio::PreSeq
        • Bio::UnivAln
        • Bio::Object, etc
        • Blast modules (currently collecting pointers!)
        • Bio::Struct (conceptual)
      • Mailing lists
        • Announcement List
        • Discussion List
        • Technical List
      • Related sites
      • Contributors and sponsors

      What's New (May 7, 1998): We present a poster at ISMB'98, see the mailing list archive.
      What's New (Dec 4, 1997): Started collecting Links to Blast modules.
      What's New (Nov 7, 1997): A response to a Request For Information of the Object Management Group, -re- Bio-objects/CORBA.
      Perl Conference Aug 19-21: A talk by Steve Brenner on Bioperl.
      What's New (July 2, 1997): We've presented a Poster at the Objects in Bioinformatics, June 1997 EBI Meeting.

      Introduction

      We develop free software, in particular for handling biosequence and alignment data. Perl is an excellent "Glue Language" for interfacing C/Fortran code, WWW/CGI, graphics, numerical analysis and much more. With the current development of a true Perl Compiler, it is a serious competitor to C: it's got high-level features, and relieves you from manual memory management, segmentation faults, bus errors, most portability problems, etc, etc.

      Current modules

      N.B. This is beta-code; in particular the interface of the Bio::PreSeq object may be revised until the first non-beta release is made. It will then be named ``Bio::Seq''.

      Bio::PreSeq, a Perl module for reading, accessing, manipulating, and analyzing single biological sequences.

      • Status: beta code, Version 0.035 from 26 MAY 1997.
      • gzipped tar file, Docu, Directory.
      • 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.
      • Planned 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 ("Pumpkin Holder"): Chris Dagdigian, cdagdigian@genetics.com.
      • Developer's site (for the newest stuff)

      May 25, 1998: Bio::UnivAln Version 1.009 is out -- PLEASE, DO MAIL ME (georg.fuellen@uni-bielefeld.de) IF YOU HAVE PROBLEMS !

      Bio::UnivAln, a Perl module for reading, parsing, writing, slicing, and manipulating multiple biosequences (sequence multisets and alignments).

      • Status: beta code, Version 1.009 from 25 May 98.

      • gzipped tar file, tar file, Docu, Code, Tests (univaln.t2) and Test output (univaln.o). (Old version: UnivAln1.006.tar).
      • Goal: Manage and manipulate multiple sequences and their alignments.
      • Very flexible slicing, mapping, consensus, (in)variable sites, gap-free sites, reverse, complement, and reverse complement.
      • Of special interest: You can specify functions for the slicing operation, e.g. use a function that returns true if column characters are "different" according to some definition of yours, and slice all the other columns off... Voila - you have the variable sites only !
      • Also, you can apply a function to some columns and/or rows, and receive the list of function values. E.g. use a function that returns the majority residue based on your own criteria, apply it to the columns, and there you go: Your consensus sequence !
      • Planned enhancements: More CGI and Graphics; improved format handling; better validity checking.
      • Chief Developer ("Pumpkin Holder"): Georg Fuellen, fuellen@Techfak.Uni-Bielefeld.DE, fuellen@dali.mathematik.uni-bielefeld.de.
      • Developer's site (for the newest stuff)

      Bio::Object, etc, a rich hierarchy which attempts to encode the underlying logic of molecular biology within a set of standard, interoperable Perl modules.

      • Status: Ongoing evolution; currently usable. Currently, we try to integrate these modules into the overall Bioperl effort -- or vice versa, depending on how you think about it ;-)
      • Goal: Provide a framework to help guide the design of interoperable Perl classes for managing and processing molecular biological data.
      • Special Features: Extensively used as part of the Saccharomyces Genome Database.
      • Chief Developer ("Pumpkin Holder"): Steven A. Chervitz, sac@genome.stanford.edu.
      • Developer's site (for the newest stuff)

      Blast Modules, for generating, parsing, and analyzing BLAST sequence analysis reports.

      • Status: Several independent implementations:
        • Updated Ian Korf's Blast module, part of the Bio::GSC distribution.
        • Steve Chervitz' Bio::Tools::Blast.pm
        • Nigel Brown's mview tool includes Blast analysis code (in the /lib/Bio/DB directory of the source distribution).
        • Alex Dong Li's webblast for NCBI blast searches (last item on page).
        • Please submit your pointer/link/code to the maintainer of this page.
      • Goal: We hope to create a consensus BLAST object that merges the functionality and design of the existing objects.

      Bio::Struct, a Perl module for reading, writing, accessing, manipulating, and analyzing biological macromolecular three dimensional structures.

      • Status: Conceptual.
      • Goal: Provide a standard and convenient representation for molecular biological structures (nucleic acids and proteins), as well as core data-management and analysis features.

      For all modules, you will need Perl 5.002 installed.

      Mailing lists

      MAILING LISTS HAVE BEEN MOVED TO THE bio.perl.org SITE !

      Related sites

      • Steve A. Chervitz' site: See Bio::Object.
      • Updated Another collection of bio-oriented perl modules at the Sanger Centre
      • Jong Park's site.
      • Will Fischer's Perl scripts.
      • Graphics: PGPERL, a Perl Interface to the PGPLOT library.
      • Fast numerical computation in Perl: Perl Data Language Homepage
      • How it all started: the original proposal, for historians only :-), and Feedback on the Bioperl Development List which is being phased out.

      Contributors and sponsors

      (Under revision.) We are loosely associated with the award-winning VSNS-BCD BioComputing Courses; some students of the 1996 course (Chris Dagdigian, Richard Resnick, Lew Gramer, and others) have contributed code and commentary, and the project is co-coordinated by Georg Fuellen, one of the VSNS-BCD organizers. Steve Chervitz is the chief coordinator; the founding coordinator is Steven Brenner.

      Back to VSNS BioComputing Division Home Page.
      This page: VSNS-BCD Copyright 1996, 1997.
      Georg Fuellen