Welcome to new developer Torsten Seemann from Victorian Bioinformatics Consortium. Torsten has taken on the role of primary maintainer of Bio::Tools::Run::StandAloneBlast.

Upgraded to mediawiki 1.5.2 – all seems to be working, but do notify us if it isn’t.

index.php is no longer part of the wiki URL. Yah! So http://bioperl.open-bio.org/wiki/Project_priority_list instead of http://bioperl.open-bio.org/wiki/index.php/Project_priority_list I also installed the interwiki table so that inter-wiki linking is much easier. See this page: http://bioperl.open-bio.org/wiki/Special:Interwiki For example to link to wikipedia you simply need to use the ‘‘‘wp’’’ prefix.

I added the Biblio plugin for mediawiki so that we could simplify how papers are referenced in our pages. I found this as part of the wikiomics project. See the help page and the Bioperl wiki publications page for examples.

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.

The Frequently Asked Questions have been entered into the Wiki and is available.

After halloween party at our house from a few years ago there was a little more public direction on who to ask for Bioperl help…

According to NCBI - BlastXML (and ASN.1) is the only guaranteed always parseable report format that is provided by their web CGI script.

I’ve started uploading some logo ideas that I’ve been playing with. Potential_Logos. These include logos for the blog front page as well as the Wiki site (and generally a BioPerl logo). O|B|F logos are welcome too.

I’ve started migrating content to the Wiki Site. I am hoping this will work out well. We need a couple of things. Decide on a theme for this site, customize it to make it a Bioperl style. Consider having a unifying style across all the O|B|F sites as Chris started doing with the foundation site.

We are pleased to announce the release of Biopython 1.41. Many improvements were made in Biopython during the eight months since the previous release, and the new release contains lots of bugfixes, improvements, new functionalities, and better documentation.