I’ve updated the wordpress install to 2.0 which has a lot more features and seems to be better setup for permissions and what not. I also upgraded the wiki to 1.5.5 to deal with some potential security holes with WMF files. I also changed the permalink structure so that the links are informative by date and post-slug. I like this much more.

The Developer Release (1.5.1) of BioPerl has been brought back into the FreeBSD Ports Collection. For instructions on how to install it, please take a look into the Getting Bioperl section of the BioPerl Wiki.

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.