Friday, April 15, 2011

BHL, DjVu, and reading the f*cking manual

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One of the many biggest challenges I've faced with the BioStor project, apart from dealing with messy metadata, has been handling page ...
Tuesday, April 12, 2011

Dark taxa: GenBank in a post-taxonomic world

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How to cite: Page, R. (2011). Dark taxa: GenBank in a post-taxonomic world. https://doi.org/10.59350/xhvv2-xjt24 In an earlier post ( Ar...
Friday, April 01, 2011

Data matters but do data sets?

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Interest in archiving data and data publication is growing, as evidenced by projects such as Dryad , and earlier tools such as TreeBASE . Bu...

Mendeley and Web Hooks

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Quick, poorly thought out idea. I've argued before that Mendeley seems the obvious tool to build a "bibliography of life." It...
Thursday, March 31, 2011

Paper on NCBI and Wikipedia published in PLoS Currents: Tree of Life

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My paper describing the mapping between NCBI and Wikipedia has been published in PLoS Currents: Tree of Life . You can see the paper here . ...
Monday, March 28, 2011

Linking the NCBI taxonomy to BBC Wildlife Finder

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A few weeks ago I spent some time mapping pages from the BBC Wildlife Finder to the equivalent taxa in the NCBI taxonomy. This seemed a use...
Friday, March 25, 2011

Fun things about crustaceans

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One side effect of playing with ways to visualise and integrate biology databases is that you stumble across the weird and wonderful stuff t...

Visualising the symbiome: hosts, parasites, and the Tree of Life

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Back in 2006 in a short post entitled "Building the encyclopedia of life" I wrote that GenBank is a potentially rich source of in...
Thursday, March 24, 2011

TreeBASE meets NCBI, again

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Déjà vu is a scary thing. Four years ago I released a mapping between names in TreeBASE and other databases called TBMap (described here: ...
Monday, March 21, 2011

Some VIZBI 2011 links

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Given that the Twitter stream tagged #vizbi will fade away soon, I've grabbed most of the links I tweeted during VIZBI 2011 and have p...
Sunday, March 20, 2011

VIZBI 2011

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I've spent the last three days at VIZBI, a Workshop on Visualizing Biological Data , held at the Broad Institute in Boston (note that ...
Friday, March 11, 2011

Geography and genes: zoomable view of frog NCBI classification with linked map

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More zoom viewer experiments (see previous post ), this time with a linked map that updates as you browse the tree (SVG-capable browser requ...
Tuesday, March 08, 2011

The Mendeley API Binary Battle - win $US 10,001

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Now we'll bring the awesome . Mendeley have announced The Mendeley API Binary Battle , with a first prize of $US 10,0001, and some very ...
Monday, March 07, 2011

Nomenclator Zoologicus meets Biodiversity Heritage Library: linking names directly to literature

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Following on from my previous post on microcitations I've blasted all the citations in Nomenclator Zoologicus through my microcitation...
Thursday, March 03, 2011

Microcitations: linking nomenclators to BHL

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One of the challenges of linking databases of taxonomic names to the primary literature is the minimal citation style used by nomenclators (...

BioStor updates on Twitter

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BioStor has had a Twitter account @biostor_org for a while, but it's not been active. I finally got around to hooking it up to BioStor...
Tuesday, March 01, 2011

Zooming a large tree, now with thumbnails

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Continuing experiments with a zoom viewer for large trees (see previous post ), I've now made a demo where the labels are clickable. If ...

Mendeley, OpenURL, BioStor, and BHL

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Mendeley has added a feature which makes it easier to use Mendeley with repositories such as BioStor and BHL . As announced in Get Full Tex...
Monday, February 28, 2011

Live demo of zooming a large tree

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After the teaser on Friday (see Deep zooming a large 2D tree ) I've put a live demo of my experiments with viewing a large tree online a...
Friday, February 25, 2011

Deep zooming a large 2D tree

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Here's a quick demo of a 2D large tree viewer that I'm working on. The aim is to provide a simple way to view and navigate very larg...