Upgraded to mediawiki 1.5.2 – all seems to be working, but do notify us if it isn’t.
About the OBF
The Open Bioinformatics Foundation (OBF) is a non-profit, volunteer-run group that promotes open source software development and Open Science within the biological research community. Membership in the OBF is free and open to anyone who wants to help promote open source or open science in a biological field.
OBF runs the annual Bioinformatics Open Source Conference (BOSC).
BOSC 2025 will be July 21-22, 2025, in Liverpool, UK (as part of ISMB/ECCB 2025). BOSC 2024 took place July 15-16, 2024, as part of ISMB 2024 in Montréal, Canada.
OBF Event Awards
The OBF Event Fellowship program aims to increase diverse participation at events promoting open source bioinformatics software development and open science in the biological research community.
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]
Biopython release 1.41
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.
[Read More]