Posts

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.

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!

It’s my great pleasure to announce the availability of the BioPerl-run packages (stable & developer releases) for the FreeBSD operating system.

For instructions on how to install BioPerl ports in FreeBSD, please take a look into the Getting Bioperl section of the BioPerl Wiki.

I’ve added a page about RSS feeds in BioPerl. These include links to CVS commits as a RSS feed. This a bit of a hack using cvs2rss and cvs2cl and I have hardcoded it to show the last 30 commits only.

In addition RSS news is now embedded on the main BioPerl and Tracking CVS commits webpages to make for better interlinking between the news and wiki site ( you might even be reading this there).

The newest summary of the BioPerl mailing lists has been posted to the wiki:

• April 12-25

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:

• April 1-11

These will likely be archived on the wiki but may be moved to a more suitable location in the future (maybe to this blog?).

I plan on starting a weekly, possibly biweekly, summary of mailing list traffic. These will be somewhat in the same vein as the Perl5 or Perl6 summaries and will be posted on the blog here and sent to the bioperl-l mail list. Barring another natural disaster here, these should start up next week (covering mail list traffic starting from April 1). The summaries will cover traffic mainly from bioperl-l (the main mail list) but will include biosql-l, since it’s fairly low traffic, and bugs/module updates from bioperl-guts-l.

GMANE has been tracking BioPerl traffic for a few years now.

You can see the page here There are several interfaces there including threaded and BLOG-like.

Those interested in tracking the mailing list in RSS readers should grab this link.

There is also a search option for the archives. Try to search GMANE for BLAST

The CVS repository is migrating from ‘pub’ to a new host called ‘dev’ and requires us to re-issue accounts. This will be a good opportunity to verify email addresses and remove unused accounts.

You should have received an email from Chris D requesting specific information and you will get a new password in the response. If not you will need to send a note to the helpdesk at support_AT_open-bio.org. The changover will happen around March 25th.