We are currently planning a timetable for the next few Bioperl releases, including the next developer release (v1.5.2), the next stable release (1.6) and beyond. Users are welcome to add requests (within reason!), donate code, etc. Lots of changes in store!
The release schedule can be found here. In order to add comments, you will be required to sign up for an account on the BioPerl wiki.
We are announcing a new Sourceforge Project called Modware. It is an object-oriented API written in Perl that creates BioPerl object representations of biological features stored in a Chado database. It basically creates a Bio::Seq object for chromosomes in Chado and creates Bio::SeqFeature::Gene objects for protein coding transcripts stored in Chado. Things like contigs are represented as Bio::SeqFeature::Generic objects. We also provide many methods for manipulating these objects once they are in memory.
[Read More]I’m glad to announce the availability of the Deobfuscator interface at the BioPerl website. You can use it at the following URL:
http://bioperl.org/cgi-bin/deob_interface.cgi
Many thanks to Laura Kavanaugh and David Messina for this great contribution to the BioPerl project!
ListSummaries for April 26-May 9 are up at the usual place:
http://www.bioperl.org/wiki/Mailing_list_summaries
Direct link:
http://www.bioperl.org/wiki/ListSummary:April_26-May_9%2C2006
It’s a bit of a hurried one so don’t be surprised to find a few spelling errors here and there. I’m getting ready for a conference in a couple weeks so I may be off the radar a bit here and there. The next ListSummary won’t be posted until May 26. Enjoy!
The newest summary of the BioPerl mailing lists has been posted to the wiki:
Post gripes, harrassments, and faint praises at the regular places.
The first of a biweekly summary of BioPerl mailing list summaries has been posted to the wiki:
These will likely be archived on the wiki but may be moved to a more suitable location in the future (maybe to this blog?).
Some discussion about changing how the RemoteBlast module behaves. If you have feedback respond to Roger’s post.
Also see these posts
Upgraded to mediawiki 1.5.2 – all seems to be working, but do notify us if it isn’t.
I’ve updated the code for Bio::Tree::Node so that each_Descendent can return the nodes in alphabetical order. This is achieved by pasing in the string ‘alpha’ (for alphabetical) or ‘revalpha’ (for reverse alphabetical). For internal nodes, they are sorted in order of the min or max (alphabetically) node in the sub-clade.
In addition, you can request the order of writing nodes by Bio::TreeIO::newick by passing in the -order_by flag which can be ‘alpha’, ‘revalpha’, ‘height’, or ‘creation’.
So you can use it like
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