BioPerl has migrated to git and GitHub!  We have also set up a mirror set of several key repositories at the great public git hosting site repo.or.cz.

If you are a current BioPerl developer (had a previous account for direct access to our prior Subversion repository), please sign up for a GitHub account and let us know your user ID.  Also, add the extra email (where ‘DEVNAME’ is your original Subversion account ID).  This should map any previous commits from the older Subversion and CVS repository to your new GitHub account.

The following are ways everyone can download the latest code.

Using git

Note you can replace ‘bioperl-live.git’ with any of the repository names (bioperl-db, bioperl-run, etc).  For BioPerl developers (GitHub collaborators) you have a choice of SSH or HTTP:

  git clone git@github.com:bioperl/bioperl-live.git

  git clone https://bioperl@github.com/bioperl/bioperl-live.git

The open read-only link (for everyone):

  git clone git://github.com/bioperl/bioperl-live.git

or using the mirror site:

  git clone git://repo.or.cz/bioperl-live.git

Using SVN (read-only)

We will also support read-only access to GitHub with Subversion.  We may allow write support at some later point.  To use svn:

  svn checkout http://svn.github.com/bioperl/bioperl-live.git

Direct downloads

Tagged releases can be found here:

http://github.com/bioperl/bioperl-live/downloads

The latest source code here:

http://github.com/bioperl/bioperl-live/archives/master

Forking BioPerl and Pull Requests

We intend on using git and GitHub to their fullest.  With that in mind, we encourage users to fork BioPerl code, make changes, commit them to your forked repository, and submit pull requests.

Documentation

We’re also in the process of updating our local developer documents for help with those who haven’t used git before.  In particular, we have a Using Git page, and have added RSS feeds for our repository commits.

Enjoy!

chris

Update: SVN version fixed, thanks to DaveMessina++ for pointing it out.

I’m pleased to announce the acceptance of OBF’s 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors:

Mark Chapman (PM Andreas Prlic) – Improvements to BioJava including Implementation of Multiple Sequence Alignment Algorithms

Jianjiong Gao (PM Peter Rose) – BioJava Packages for Identification, Classification, and Visualization of Posttranslational Modification of Proteins

Kazuhiro Hayashi (PM Naohisa Goto) – Ruby 1.9.2 support of BioRuby

Sara Rayburn (PM Christian Zmasek) – Implementing Speciation & Duplication Inference Algorithm for Binary and Non-binary Species Tree

Joao Pedro Garcia Lopes Maia Rodrigues (PM Eric Talevich) – Extending Bio.PDB: broadening the usefulness of BioPython’s Structural Biology module

Jun Yin (PM Chris Fields) – BioPerl Alignment Subsystem Refactoring

Congratulations to our accepted students!

All told, we had 52 applications submitted for the 6 slots (5 originally assigned, plus 1 extra) allotted to us by Google.  Proposals were extremely competitive: 6 out of 52 translates to an 11.5% acceptance rate.  We received a lot of really excellent proposals, the decisions were not easy.

Thanks very much to all the students who applied, we very much appreciate your hard work.

Here’s to a great 2010 Summer of Code, I’m sure these students will do wonderful work.

Rob Buels
O|B|F GSoC 2010 Administrator

BioPerl developers and users attended the BioPerl satellite meeting on January 13th, just prior to the GMOD Meeting.  Several items were covered on the agenda:

• In order to start addressing whole genome data with more lightweight objects, we are planning on setting up a lightweight Bio::SeqI object that has a flexible DB backend (i.e. Bio::DB::SeqFeature::Store or similar).  We are also contemplating adding lazy parsing for some parsers, possibly using the Bio::PullParserI methods (or similar) that Sendu Bala created.
• After a final  1.6 branch point release, we may ‘freeze’ BioPerl in a maintenance mode, primarily so that we can reorganize core into several more easily installed subdistributions on a branch.  New modules will essentially be additional separate repos that will depend on BioPerl core.  This reorganization has been discussed for a few years now, and as we edge closer to starting this (probably this spring) we’ll announce more details.
• Some initial thoughts on how to handle circular genomes more efficiently.  We essentially do this already, but it isn’t full-proof.
• Need some significant time dedicated towards GFF3-based coding (reimplement FeatureIO but allow some flexibility).  Rob Buels had started the initial run at splitting out FeatureIO, so next step is a true reimplementation.
• We don’t plan on including Moose support for the immediate future, feeling that it would be better to reimplement some of the classes from scratch using Moose and similar as a BioPerl 2.0, or possibly await the impending Rakudo Perl 6 alpha and start afresh using that instead of Moose.

Anything we missed?  Anything you would like to address?  Please add comments and we’ll discuss them on list.

I’m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the conventions agreed by the OBF projects:

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
Peter J. A. Cock (Biopython), Christopher J. Fields (BioPerl), Naohisa Goto (BioRuby), Michael L. Heuer (BioJava) and Peter M. Rice (EMBOSS).
Nucleic Acids Research, doi:10.1093/nar/gkp1137

This will hopefully serve as a reference describing the original standard Sanger FASTQ, and the two variants from Solexa/Illumina, and how to inter-convert between them.

Two of the core BioPerl developers, Jason Stajich and Chris Fields, were interviewed by FLOSS Weekly.  The interview is now available as an MP3 on the FLOSS Weekly website; several streaming versions (including podcast) are also available.

BioPerl 1.6.1 is now available for ActivePerl as a PPM, instructions for downloading can be found on the BioPerl wiki. This has been tested only for ActivePerl 5.10 and above, so any feedback with older versions of BioPerl would be greatly appreciated.

Running a bit late on this, so just a quick note that the first alphas for BioPerl-Run, BioPerl-DB, and BioPerl-Network have been uploaded to CPAN:

• BioPerl-Run
• BioPerl-DB
• BioPerl-Network

They can also be downloaded from the BioPerl website:

http://bioperl.org/DIST/RC/

This is the first run where we’ve switched to a regular Module::Build installation, so expect some initial bumps! There are a few initial problems that I plan on addressing soon, the main one being none of the modules are assigned version numbers (this may be a consequence of not pulling the version from a specific module). The other, more serious one, is that the Build.PL script checks for DBI but isn’t checking for any compatible DBD::* adaptors for BioPerl-DB (so it fails tests if DBI is installed). We have code in core to check for DBI drivers, so I may adapt that for BioPerl-DB.

Enjoy!

chris

We are pleased to announce the immediate availability of BioPerl 1.6.1, the latest release of BioPerl’s core code. You can grab it here:

Via CPAN:

http://search.cpan.org/~cjfields/BioPerl-1.6.1/

Via the BioPerl website:

http://bioperl.org/DIST/BioPerl-1.6.1.tar.bz2
http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz
http://bioperl.org/DIST/BioPerl-1.6.1.zip

The PPM for Windows should also finally be available this week, ActivePerl problems permitting (we will post more information when it becomes available).

Tons of bug fixes and changes have been incorporated into this release. For a more complete change list please see the ‘Changes’ file included with the distribution.

A few highlights:

• FASTQ parsing and interconversion of the three FASTQ variants (Sanger, Illumina, Solexa) now works (a concerted OBF effort!)
• Significant refactoring of Bio::Restriction methods
• Complete refactoring of Bio::Search-related tiling code, including HOWTO documentation
• GBrowse-related fixes:
• - berkeleydb database now autoindexes wig files and locks correctly
• - add Pg, SQLite, and faster BerkeleyDB implementations
• Infernal 1.0 output is now parsed
• New SearchIO-based parser for gmap -f9 output
• BLAST XML parsing essentially complete
• Installation via CPANPLUS should now work
• For those using Strawberry Perl on Windows, the latest build is expected to pass all tests.
• ‘raw’ sequence format now parsed by line or optionally as a single sequence
• SCF parsing/writing now round-trips
• Demo code for using RPS-BLAST and Bio::Tools::Run::RemoteBlast
• Bio::Tools::SeqPattern now has a backtranslate() method
• Bio::Tree::Statistics now has methods to calculate Fitch-based score, internal trait values, statratio(), sum of leaf distances
• Scripts
• - update to bp_seqfeature_load for SQLite
• - hivq.pl – commmand-line interface to Bio::DB::HIV
• - fastam9_to_table – fix for MPI output
• - gccalc – total stats
• - einfo – simple script to find up-to-date NCBI databases, list field and link values for a specific database

We will shortly release updates for BioPerl-db, BioPerl-run, and BioPerl-network. Enjoy!

chris

All,

I am proud to announce that the 1.6 release for BioPerl-run, BioPerl-
db, and BioPerl-network are now available by direct download and via
CPAN. These are designated as 1.006000, with a requirement for
BioPerl 1.6 and higher (1.006000).

FIXED:

1) Bio::Tools::Run::Primer3 now accepts primer3 or primer3_core as
executable names
2) Bio::Tools::Run::Vista tests now pass if Vista.jar is installed.
3) bug fix in bioperl-network

What remains for the 1.6 release series:

* Documentation, Documentation, and Documentation. I haven’t had much
time unfortunately to work on documentation, primarily for BUGS/
INSTALL/README etc within db/run/network (the latter has been mainly
updated by Brian O.) I will attempt to update these for the next
point release, tentatively scheduled for mid-April.

NOTE (so there is no confusion): the BioPerl-run archive is designated
as BioPerl-1.6.1.tar.gz. This is due to a small off-by-one bug in the
test suite that passed for me locally but fails if primer3 isn’t
installed. This unfortunately required a reupload to PAUSE. However,
the minimal core version version required is still 1.006000.

Related to the above, I will sort out the versioning issues for the
next point release as we arrive closer to it. If needed we can bump
the point release up to 1.6.2 to bring everything in sync.

Here they are!

BioPerl-run:

http://bioperl.org/DIST/BioPerl-run-1.6.1.tar.bz2

http://bioperl.org/DIST/BioPerl-run-1.6.1.tar.gz

http://bioperl.org/DIST/BioPerl-run-1.6.1.zip

BioPerl-db:

http://bioperl.org/DIST/BioPerl-db-1.6.0.tar.bz2

http://bioperl.org/DIST/BioPerl-db-1.6.0.tar.gz

http://bioperl.org/DIST/BioPerl-db-1.6.0.zip

BioPerl-network:

http://bioperl.org/DIST/BioPerl-network-1.6.0.tar.bz2

http://bioperl.org/DIST/BioPerl-network-1.6.0.tar.gz

http://bioperl.org/DIST/BioPerl-network-1.6.0.zip

SIGNATURES:

http://bioperl.org/DIST/SIGNATURES.md5

Cheers!

chris