Welcome to new developer Torsten Seemann from Victorian Bioinformatics Consortium. Torsten has taken on the role of primary maintainer of Bio::Tools::Run::StandAloneBlast.
media wiki upgraded
Upgraded to mediawiki 1.5.2 – all seems to be working, but do notify us if it isn’t.
no more index.php
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]].
Biblio plugin for wiki
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.
sort order for Bio::Tree::Node each_Descendent
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
[Read More]FAQ updated
The Frequently Asked Questions have been entered into the Wiki and is available.
Seen on the road
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…
Getting BlastXML using RemoteBlast
According to NCBI - BlastXML (and ASN.1) is the only guaranteed always parseable report format that is provided by their web CGI script. Here is some code to specify how the data should be requested (and perhaps this will become the default).
[Read More]
Logo Ideas
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
New Wiki Content
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.
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.
[Read More]