Biopython, Numeric and numpy

 Posted on September 22, 2008  |  peterc

To date, Biopython releases have relied on the original numerical python library, Numeric (used in python with “import Numeric”). In the next release we will at last be moving to its successor, NumPy (used in python with “import numpy”). This transition is already under way in the Biopython source code repository. For further details, or to voice your opinion or enthusiasm, please join the Biopython Mailing List(s). Finally, for anyone interested in the background story, the SciPy project has a page describing the history of the numerical python libraries. [Read More]

Hey what’s happening?

 Posted on July 10, 2007  |  stajich

So Mailing list summaries have stopped because we need someone else to help post these summaries. Not a light job unfortunately. If you are interested, please post to the mailing list or contact Jason, Sendu, or Chris for more details. This is one way you can help BioPerl without contributing code if you aren’t comfortable with that type of commitment. Two things that have been discussed on the mailing list lately are: [Read More]

BioPerl-run in FreeBSD

 Posted on May 2, 2006  |  mauricio

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.

BioPerl Mailing List Summaries

 Posted on April 11, 2006  |  cjfields

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?).

Weekly Mailing List Traffic Summaries

 Posted on April 5, 2006  |  cjfields

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. [Read More]

Developer accounts re-issued

 Posted on March 24, 2006  |  stajich

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 clean version. Note that before (and sometime ON) the 25th of March anything that is committed to the dev machine CVS repository will likely get wiped out so it is best to either hold off commits on the 25th or keep copies of stuff around. [Read More]

BioPerl on Mac OS X using fink

 Posted on January 30, 2006  |  mauricio

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, Windows, etc.) to put in the wiki the necessary documentation about installing BioPerl and Perl modules in your favorite OS/distributions. [Read More]