Bioperl: Bioperl 0.6 Released

[Ewan Birney]

   Announcing bioperl 0.6 release
   ------------------------------


The bioperl developers are delighted to announce the bioperl 0.6
release. The 0.6 release is the latest stable release, replacing the
old 0.05.1 release. Bioperl is coordinated from http://bio.perl.org.
Please visit the web site for more details about the project


The release is available from 

  ftp://bio.perl.org/pub/DIST

as a set of CPAN modules (bioperl-0.6.tar.gz and bioperl-ext-0.6.tar.gz)

The releases are also available from CPAN. Please check out your
nearest CPAN mirror site (http://www.cpan.org/ for the top level).


The bioperl-0.6 is the main distribution. The bioperl-ext is an
additional distribution with compiled C extensions. bioperl-ext is not
needed for the majority of the functionality of bioperl-0.6.


The installation process is a standard CPAN module, requiring the commands

  perl Makefile.PL 
  make
  (make test - optional)
  make install

The README has more details on this.


The 0.6 release as the following new or improved functionality:


   o Sequences can have Sequence Features attached to them
        - The sequence features can be read from or written to
          EMBL and GenBank style flat files

   o Objects for Annotation, including References (but not
     full medline abstracts), Database links and Comments are
     provided

   o A Species object to represent nodes on a taxonomy tree
     is provided

   o The ability to parse HMMER and Sim4 output has been added

   o The Blast parsing has been improved.

   o Flat file indexed databases provide both random access 
     and sequential access to their component sequences.

   o A CodonTable object has been written with all known 
     CodonTables accessible.

   o A number of new lightweight analysis tools have been
     added, such as molecular weight determination.


The 0.6 release also has improved software engineering

  
   o The sequence objects have been rewritten, providing more
     maintainable and easier to implement objects. These
     objects are backwardly compatible with the 0.05.1 objects

   o Many objects are defined in terms of interfaces and then  
     a Perl implementation has been provided. The interfaces
     are found in the 'I' files (module names ending in 'I').

     This means that it is possible to wrap C/CORBA/SQL access
     as true "bioperl" objects, compatible with the rest of
     bioperl.

   o The SeqIO system has been overhauled to provide better
     processing and perl-like automatic interpretation of <>
     over arguments.

   o Many more tests have been added (a total of 172 automatic
     tests are now run before release).



Comments, praise or annoyances should be directed to the 
bioperl-guts list (vsns-bcd-perl-guts@lists.uni-bielefeld.de).


Bugs should be entered through the bug tracking interface
found at http://bio.perl.org/bioperl-bugs/.



Ewan Birney (on behalf of the bioperl developers).






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