Monthly Archives: November 2005

media wiki upgraded

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

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no more index.php

index.php is no longer part of the wiki URL. Yah! So instead of I also installed the interwiki table so that inter-wiki linking is much easier. See this page: For example to link to wikipedia you simply … Continue reading

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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.

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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 … Continue reading

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FAQ updated

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

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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…

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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 … Continue reading

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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

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