Friday, December 07, 2012

Elsevier articles have interactive phylogenies

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Say what you will about Elsevier, they are certainly exploring ways to re-imagine the scientific article. In a comment on an earlier post F...
Thursday, December 06, 2012

NEXUS parser and tree viewer in Javascript

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Following on from the SVG experiments I've started to put some of the Javascript code for displaying phylogenies on Github. Not a repos...
Wednesday, December 05, 2012

The Tree of Life

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The following poem by David Maddison was published in Systematic Biology ( doi:10.1093/sysbio/sys057 ) under a CC-BY-NC license. I think th...
Tuesday, December 04, 2012

Viewing phylogenies on the web: Javascript conversion of Newick tree to SVG

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Quick test of an idea I'm playing with. By embedding a Newick-format tree description in HTML and adding some Javascript I can go from t...
Wednesday, November 28, 2012

ZooBank data model

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I'm trying to get my head around the data model used by ZooBank to store taxonomic names. To do this, I've built a graph for the sp...
Tuesday, November 27, 2012

Fuzzy matching taxonomic names using ngrams

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Quick note to self about possible way to using fuzzy matching when searching for taxonomic names. Now that I'm using Cloudant to host C...
Thursday, November 22, 2012

BioStor in the cloud

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Quick note on an experimental version of BioStor that is (mostly) hosted in the cloud. BioStor currently runs on a Mac Mini and uses MySQL ...
Wednesday, November 21, 2012

Species wait 21 years to be described - show me the data

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Benoît Fontaine et al. recently published a study concluding that average lag time between a species being discovered and subsequently desc...
Monday, October 22, 2012

Resolving free-form citations

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We don't need no stinkin' parser- a guide to resolving free-form citations with #CrossRef Metadata Search -> goo.gl/f9a4e — Geof...
Friday, October 19, 2012

The failure of phylogeny databases

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Only 4% of all published phylogenies have data in #treebase or @ datadryad — Karen Cranston (@kcranstn) October 18, 2012 It is well known t...
Wednesday, October 17, 2012

OneZoom

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James Rosindell's OneZoom tree viewer is out and the paper describing the viewer has been published in PLoS One (disclosure, I was a re...
Friday, October 12, 2012

Mapping evolutionary biology: @evoldir and #ProjectEvoMap

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Robert M. Griffin ( @GriffinEvo ) has launched ProjectEvoMap . Rob explains: I have decided this week to try to create a resource where evol...
Friday, September 28, 2012

Reading the Biodiversity Heritage Library using Readmill

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tl;dr Readmill might be a great platform for shared annotation and correction of Biodiversity Heritage Library content. Thinking about acc...
Monday, September 24, 2012

Towards a biogeographic search engine

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We all have a "past" that we might not advertise widely, and my past includes flirting with panbiogeography. Indeed my PhD thesis ...
Saturday, September 22, 2012

Touching the tree of life

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Prompted by a conversation with Vince Smith at the recent Online Taxonomy meeting at the Linnean Society in London I've been revisiting...
Saturday, September 08, 2012

Decoding Nature's ENCODE iPad app - OMG it's full of ePUB

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The release of the ENCODE (ENCyclopedia Of DNA Element) project has generated much discussion (see Fighting about ENCODE and junk ). Perhaps...
Wednesday, September 05, 2012

BHL is duplicating DOIs because it doesn't know about articles

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Quick note that as much as I like that the Biodiversity Heritage Library is using DOIs, they are generating them for publications that alrea...
Thursday, August 02, 2012

Google Knowledge Graph using data from BBC and Wikipedia

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Google's Knowledge Graph can enhance search results by display some structured information about a hit in your list of results. It'...
Tuesday, July 24, 2012

Dear GBIF, please stop changing occurrenceIDs!

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If we are ever going to link biodiversity data together we need to have some way of ensuring persistent links between digital records. This ...
Monday, July 23, 2012

Microbiome as climate, macrobiome as weather, and a global model of biodiversity

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Half-baked idea time. Thinking about projects such as the Earth Microbiome Project and Genomic Observatories , the recent GBIC2012 meeting...