Archive for the ‘Development’ Category
Thursday, May 18th, 2006
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 ...
Posted in Code | No Comments »
Sunday, May 14th, 2006
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!
Posted in Code, Development, Documentation | No Comments »
Wednesday, May 10th, 2006
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 ...
Posted in Code | No Comments »
Tuesday, May 2nd, 2006
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.
Posted in Development, Documentation | No Comments »
Tuesday, April 25th, 2006
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.
Posted in Code, Community, Development, Documentation, Mailing lists, Website | No Comments »
Tuesday, April 11th, 2006
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?).
Posted in Code, Community, Development, Documentation, Mailing lists | 2 Comments »
Wednesday, April 5th, 2006
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 ...
Posted in Community, Development, Documentation, Mailing lists, Website | No Comments »
Thursday, March 23rd, 2006
We are moving developer repository to a new server which will require you to get a new developer account.
To fix your local repository you should be able to run this on your local repository:
$ find bioperl -name 'Root' | xargs perl -i.backup -p -e 's/pub\.open/dev.open/'
or just check out a ...
Posted in Development | No Comments »
Tuesday, February 7th, 2006
Some discussion about changing how the RemoteBlast module behaves. If you have feedback respond to Roger's post.
Also see these posts
Chris Field's post (1)
Chris Field's post (2)
Roger volunteering to take on maintenance
Posted in Code, Development | 2 Comments »
Monday, January 30th, 2006
Instructions on how to install BioPerl on Mac OS X have been added to the Wiki, specifically at the Getting Bioperl section. Thanks to Koen van der Drift for contributing with this info.
We continue to encourage people who is taking care of creating packages for other platforms (specific Linux distributions, ...
Posted in Development, Documentation | No Comments »