Monday, January 30, 2012

BLAST a sequence and get a tree

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For this weeks sessions of my phyloinformatics course I'm developing some phylogeny tools. The first is a simple AJAX-based BLAST tool....
Thursday, January 26, 2012

Extracting museum specimen codes from text

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Quick note about a tool I've cobbled together as part of the phyloinformatics course , which addresses a long standing need I and others...
Monday, January 23, 2012

Open course on phyloinformatics

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As part of a postgraduate course here at the University of Glasgow I'm teaching five sessions on "phyloinformatics", which I...
Thursday, January 19, 2012

EOL iPad web app using jQueryMobile

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As part of a course on "phyloinformatics" that I'm about to teach I've been making some visualisations of classifications....
Wednesday, January 18, 2012

Yet another reason why we need specimen identifiers, now!

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This message appeared on the TAXACOM mailing list: It is getting more and more necessary for taxonomists to demonstrate that they are usefu...
Tuesday, January 17, 2012

Mendeley as CiteBank: some ideas

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Here are some quick notes on how BHL could use Mendeley as a "CiteBank". As a repository of bibliographic data If the goal is to a...
Tuesday, January 10, 2012

Journals I'd like BHL to scan

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I've recently updated my database of links between animal taxonomic names and literature identifiers , which now has over 280,000 names ...
Monday, December 19, 2011

Towards an interactive taxonomic article: displaying an article from ZooKeys

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One of the things I keep revisiting is the way we display scientific articles. Apart from Nature's excellent iPhone and iPad apps, most...
Monday, December 12, 2011

Exporting data from Australian Faunal Directory on CouchDB

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Quick note to self about exporting data from my Australian Faunal Directory on CouchDB project. To export data from a CouchDB view you can ...
Sunday, December 11, 2011

DNA Barcoding, the Darwin Core Triplet, and failing to learn from past mistakes

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Given various discussions about identifiers, dark taxa, and DNA barcoding that have been swirling around the last few weeks, there's one...
Tuesday, December 06, 2011

Google doesn't like BioStor anymore

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According to Google Analytics BioStor has experienced a big drop in traffic since the start of October: At one point I'm getting someth...
Monday, December 05, 2011

These are my species - finding the taxonomic names I published using Mendeley

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The latest addition to my mapping of taxonomic names to the literature ( http://iphylo.org/~rpage/itaxon/ ) is the ability for authors with ...
Tuesday, November 29, 2011

Mapping names to literature: closing in on 250,000 names

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Following on from my earlier post Linking taxonomic names to literature: beyond digitised 5×3 index cards I've been slowly updating my ...

Towards the bibliography of life

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David King et al.'s paper "Towards the bibliography of life" http://dx.doi.org/10.3897/zookeys.150.2167 has just appeared in ...
Thursday, November 24, 2011

BHL needs to engage with publishers (and EOL needs to link to primary literature)

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Browsing EOL I stumbled upon the recently described fish Protoanguilla palau , shown below in an image by rairaiken2011 : Two things struck...
Wednesday, November 23, 2011

Wikipedia History Flow tool now in GitHub

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Inspired by a comment on my post Visualising edit history of a Wikipedia page , the code I use to make history flow diagrams like the one be...
Tuesday, November 22, 2011

Apache mod_rewrite and question marks "?"

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Quick note to self in case I (inevitably) forget later. If you are using Apache mod_rewrite to make nice, clean URLs, and are also supportin...
Friday, November 18, 2011

Adding article-level metadata to BHL

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Recently I've been thinking about the best ways to make article-level metadata from BioStor more widely available. For example, for som...

Nature iPhone app clone in GitHub

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One thing I'm increasingly conscious of is that I've a lot of demos and toy projects hanging around and the code for most of these i...
Friday, October 28, 2011

Sherborn presentation on Open Taxonomy

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Here is my presentation from today's Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond meeting. Open tax...