A PopGen HOWTO added to the website for using the population genetics modules in Bioperl.
The PAML HOWTO is in-process of being updated to describe the new functionalilty.
Beginners HOWTO
Brian Osborne and James Thompson have written a Bioperl HOWTO for beginners, for those who are interested in learning about Bioperl but have done very little programmming. Topics include creating a Sequence object, I/O and files, retrieving from Genbank, and using the Sequence object.
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Bioperl 1.5.0 released
Bioperl 1.5.0 Developer’s release is available for download.
http://bioperl.org/DIST/bioperl-1.5.0.tar.bz2 425ac55ecbb4339b7b532ba6d429bb40
http://bioperl.org/DIST/bioperl-1.5.0.tar.gz 172472f0675de9a583432e21c9b1b5fc
http://bioperl.org/DIST/bioperl-1.5.0.zip 3febcd2445a7393c65981a6f9f13a9ed
We’ll update the website to reflect this new release.
The odd-numbered releases are called developer releases and are not deposited on CPAN. Please note that the API in 1.5.0 may change before the 1.6.0 release. which will be consider a stable API. We may do another developer release before 1.6.0 goes out.
Lots of people have contributed to this release, I apologize for not naming them all. I’ll try to cover some: thanks to Aaron Mackey for getting this release started, Brian Osborne for extensive documentation improvements, Nathan Haigh for volunteering to make a PPM of the release and Barry Moore and Nathan answering many of the windows related questions, Allen Day & Scott Cain & Steffen Grossmann for the work on FeatureIO, GFF3, and SeqFeature::Annotated, Chris Mungall for the work with Unflattener to merge GenBank annotations into GFF3 objects.
Please see the AUTHORS file for a complete list of contributors.
Jason Stajich on behalf of the Bioperl developers.
http://portal.open-bio.org/pipermail/bioperl-l/2005-January/018031.html
[Read More]Bioperl 1.5 RC 2
Release candidate 2 of Bioperl 1.5.0 is ready for downloading and testing. Please report back to the bioperl list with any problems. We would like to make a developer release by the end of January 2005.
Bioperl 2005 Summary
I just wanted to use the end of the year as a chance to reflect on what
we’ve accomplished in 2004 and think about what 2005 holds for Bioperl.
List Message
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Bioperl preparing 1.5 release
Bioperl developers are preparing a 1.5 release, you can grab the pre-release for testing at http://bioperl.org/DIST. We would greatly appreciate you downloading and testing this code before it is released by running ‘make test’.
See Aaron’s post announcing the RC1 candidate.
Bioperl Bootcamp June 21-25
Continuing on the BioJava Bootcamp of 2003, The Quebec Bioinformatics Network (BioneQ) is organizing its first BioPerl Bootcamp, to be held at the Universite de Montreal from June 21-25 2004.
The invited speakers are leaders in the use of Perl in bioinformatics and development of BioPerl:
Aaron Mackey (U. of Pennsylvania) Jason Stajich (Duke University) Lincoln Stein (Cold Spring Harbor Labs)
Seminars and exercise sessions will be in a Linux computer lab for a total hands-on experience.
[Read More]Bioperl 1.4 for Windows
Bioperl version 1.4 for Windows is available. Thanks once again to Nigam Shah for creating and testing the PPM and PPD files.
BioKnoppix
BioKnoppix is a new live CD linux, based on KNOPPIX, with EMBOSS 2.8.0, jemboss, artemis, clustalx, Cn3D, ImageJ, BioPython, Rasmol, Bioperl, Bioconductor. It being made available by The University of Puerto Rico High Performance Computing facility (HPCf) and the Puerto Rico Biomedical Research Infrastructure Network (BRIN-PR). Great stuff!
Bioperl Release 1.4
The stable Bioperl release 1.4 is available for immediate use at: http://bioperl.org/DIST.
We are releasing simultaneously three modules:
They will also appear shortly at the IUBIO mirror (later today) and in CPAN.
Remember, all the external modules needed by bioperl-core can be installed from CPAN under name Bundle-BioPerl.
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