Bioperl 1.0 Release Announcement
I am pleased to
announce the release of verision 1.0 of the Bioperl toolkit. This release
represents what we believe to be feature complete for most biological
sequence manipulations in bioinformatics. A great deal of work has gone
into this project from its start in 1995 as a collection of modules
for sequences and alignments to its transition to a more formal Object
Oriented framework which has allowed for easier extensibility for the
myriad of data formats in the realm of bioinformatics. Work in the past
year has seen an explosion of new areas of interest by developers as
well as a commitment to stability and an easy to use programming interface.
This release of the toolkit contains modules for representing biological
sequences, protein structure, sequence alignments, BLAST and FastA reports,
biological maps, sequence features and their locations including complex
locations, annotations & bibliographic references, phylogenetic
trees, and gene structures. Included in the kit are tools to visually
render sequences, build and access local sequence indexes, parse and
output most major biological sequence formats, access to bibliographic
query access to remote sequence databases over the web, input and output
of biological maps, and support for phylogenetic trees. Additionally
the toolkit supports representations of sequence variations and mutations
to allow a programming interface to sequences with variable residues.
This release would not have been possible without the hard work of all
the members of the project. These include the Bioperl Core: Ewan Birney,
Chris Dagdigian, Hilmar Lapp, Heikki Lehvaslaiho, Jason Stajich, and
Lincoln Stein. Significant contributions of code, debugging, and suggestions
were made by all the members of the project and list subscribers especially:
Dave Block, Kris Boulez, Steve Chervitz, Michele Clamp, James Cuff,
Allen Day, James Diggans, Aaron Mackey, Chris Mungall, Brian Osborne,
Peter Schattner, Martin Senger, Elia Stupka, and Mark Wilkinson. Additionally
the project has recieved help from many of the mailing list subscribers
and bioperl users with their suggestions and questions which has helped
development effort. The project has also greatly benefited from the
cross-talk between the Biopython and BioJava projects and we'd like
to acknowledge their support and idea sharing.
We'd also like to thank especially thank Brian Osborne and Peter Schattner
for their work in getting the documentation and Bioperl Tutorial updated
for all the new modules and features.
Jason Stajich on behalf of the Bioperl Core.
The release is available at http://www.bioperl.org/DIST/bioperl-1.0.tar.gz
or from the website http://www.bioperl.org/
and will be available from CPAN in the coming week.
Please see the INSTALL and README documents for information about installing
and cross-platform compatibilities.
The code is released under the Perl Artistic License which is included
in the distribution file.
Bioperl is supported by the Open Bioinformatics Foundation
which provides infrastructure for the projects.
YOUR FEEDBACK HELPS US
You can provide feedback to the project and help us estimate the number
of users the project has by responding to the bioperl survey. Go to
to help us gauge how useful the toolkit is to your work and where we
can make improvements to address new areas of computational biology
1.0.0 Major Stable Release
This represents a major release of bioperl with significant improvements
over the 0.7.x series of releases.
contains modules for Bibliographic data.
Bio::DB::Biblio contains the query modules. Additionally one can parse
medlinexml from the ebi bibliographic query service (BQS)
system and Pubmed xml from NCBI. See Martin Senger's documentation in
Bio::Biblio for more information.
is a sequence database registry part of Open Bioinformatics Database
Access. Additionally Bio::DB::Flat was
introduced to support the cross-project OBDA standard for indexed flatfiles.
information. This project is under active development so the modules
in this release represent preliminary implementations.
In-Memory Sequence caching is provided by Bio::DB::InMemoryCache and
Bio::DB::FileCache which acts like a
for rendering sequences as PNG,JPG, or GIFs has been added by Lincoln
XEMBL SOAP service
access in provided in Bio::DB::XEMBL.
Bio::MapIO for biological map navigation and a framework afor parsing
executing EMBOSS programs locally in Bio::Factory::EMBOSS
Future work will integrate Pasteur Institute's Pise and EBI's openBSA
analysis queues for remote analysis.
and Bio::Annotation::Collection introduced as new objects for handling
information (dblinks, references, etc) and is more robust that previous
annotation handling object.
was introduced to support an extensible framework for sequence database
search results. Currently blast, NCBI XML blast format (-m 7), and FastA
parsing are implemented. The Bio::Search objects were added to represent
the Result, Hit, and
HSP objects retrieved from a search. To support this new direction Bio::Tools::Blast
is officially deprecated.
system allows output of Bio::Search objects in a tabular or HTML form.
is Lincoln Stein's database implementation of GFF files which can be
used for DAS backends and is part of the Generic Model Organism Database
Bio::TreeIO namespaces and modules were added to support representation
and parsing of phylogenetic trees.
as added in 0.9.1 and includes a pdb parser and objects to represent
Sequence formats have been added for parsing or writing.
trunc() and subseq() in Bio::PrimarySeqI now accepts
Bio::LocationI objects as well as start/end.
now supports two methods for calculating average and overall percentage
was achieved in SeqIO genbank and embl parsers, future releases will
focus on an event based parsing system
where we hope to achieve improved parsing speeds.
A FAQ has been
started and is included in the release to provide a starting point for
frequent questions and issues.
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