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. For example [[wp:Bioinformatics]] or else the wikiomics site [[wikiomics:BLAST]].

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.

In addition, you can request the order of writing nodes by Bio::TreeIO::newick by passing in the -order_by flag which can be ‘alpha’, ‘revalpha’, ‘height’, or ‘creation’.

So you can use it like

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…

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.

-jason

I’ve started migrating content to the Wiki Site. I am hoping this will work out well. We need a couple of things.

1. 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.

2. Generate a project image (or several that can be rotated) for the header on the site, something with a camel and DNA and images of phylogenetic trees and BLAST searches would be cool.

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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. To pick a few, there’s the new Bio.MEME module by Jason Hackney, updates to the Blast parser using Bertrand Frottier’s NCBIXML code, a BLAT parser by Yair Benita, numerous updates in Bio.PDB, CompareACE support in AlignAce, and improved user-friendliness in Bio.Seq.