[Bioperl-l] Bioperl 1.0 Released
Jason Stajich
jason@cgt.mc.duke.edu
Mon, 18 Mar 2002 12:53:26 -0500 (EST)
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 services, 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 shaped the
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
ftp://bioperl.org/pub/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
(www.open-bio.org) 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 http://bioperl.org/survey.html 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 and bioinformatics.
ChangeLog
-------------------
1.0.0 Major Stable Release
This represents a major release of bioperl with significant
improvements over the 0.7.x series of releases.
o Bio::Biblio 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.
o Bio::DB::Registry 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. See http://obda.open-bio.org for more
information. This project is under active development so the
modules in this release represent preliminary implementations.
o File-based and In-Memory Sequence caching is provided by
Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
local database.
o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
been added by Lincoln Stein.
o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
o Bio::Map and Bio::MapIO for biological map navigation and a
framework afor parsing them in.
o Interface for 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.
o Bio::AnnotationCollectionI and Bio::Annotation::Collection
introduced as new objects for handling Sequence Annotation
information (dblinks, references, etc) and is more robust that
previous annotation handling object.
o Bio::SearchIO 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.
o Bio::SearchIO::Writer system allows output of Bio::Search
objects in a tabular or HTML form.
o Bio::DB::GFF 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 project (http://gmod.sourceforge.net).
o Bio::Tree and Bio::TreeIO namespaces and modules were added to
support representation and parsing of phylogenetic trees.
o Bio::Structure as added in 0.9.1 and includes a pdb parser and
objects to represent protein structure.
o More Multiple Sequence formats have been added for parsing or writing.
o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
Bio::LocationI objects as well as start/end.
o Bio::SimpleAlign now supports two methods for calculating
average and overall percentage identity.
o 30% speedup 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.
o A FAQ has been started and is included in the release to provide
a starting point for frequent questions and issues.
--
Jason Stajich
Duke University
jason@cgt.mc.duke.edu