Enhanced display of scientific articles using extended metadata
Although the Web has transformed science publishing, scientific papers themselves are still essentially “black boxes”, with much of their content intended for human readers only. Typically, comput…
Received 24 April 2009 16:36 UTC; Posted 24 April 2009
Posted to: Ecology, Bioinformatics, Evolutionary Biology
bioGUID: resolving, discovering, and minting identifiers for biodiversity informatics
Linking together the data of interest to biodiversity researchers (including specimen records, images, taxonomic names, and DNA sequences) requires services that can mint, resolve, and discover glo…
Received 17 April 2009 17:21 UTC; Posted 17 April 2009
Posted to: Bioinformatics
On The Dangers Of Aligning RNA Sequences Using “Conserved” Motifs
Aligning RNA sequences can be a challenging task. Automatic sequence alignment programs typically align sequences only with respect to primary sequence, and as a result may yield spurious alignment…
Received 18 September 2007 09:05 UTC; Posted 18 September 2007
Posted to: Bioinformatics, Evolutionary Biology
Treemap Versus BPA (Again): A Response to Dowling
TreeMap is a computer program for analysing host-parasite cospeciation. We respond to Dowling’s (Cladistics, 18: 416-435) recent comparison of TreeMap and Brooks Parsimony Analysis (BPA) by showing…
Received 18 September 2007 09:09 UTC; Posted 18 September 2007
Posted to: Bioinformatics, Evolutionary Biology
Towards a Taxonomically Intelligent Phylogenetic Database
This note outlines some of the key intellectual obstacles that stand in the way of creating a usable phylogenetic database. These challenges include the need to accommodate multiple taxonomic names…
Received 18 September 2007 09:01 UTC; Posted 18 September 2007
Posted to: Bioinformatics, Evolutionary Biology
Visualising a scientific article
This paper describes my entry in the Elsevier Grand Challenge “Knowledge Enhancement in the Life Sciences” contest. The entry takes a collection of fulltext issues of _Molecular Phylogenetics and …
Received 28 November 2008 16:15 UTC; Posted 28 November 2008
Posted to: Ecology, Bioinformatics
Towards realising Darwin’s dream: setting the trees free
The fact that all living organisms are related by common descent is one of the central principles of modern biology. Since the early 1990’s the amount of data available to evolutionary biologists …
Received 21 August 2008 20:29 UTC; Posted 22 August 2008
Posted to: Ecology, Bioinformatics
Biodiversity informatics: the challenge of linking data and the role of shared identifiers
A major challenge facing biodiversity informatics is integrating data stored in widely distributed databases. Initial efforts have relied on taxonomic names as the shared identifier linking records…
Received 03 April 2008 16:51 UTC; Posted 03 April 2008
Posted to: Ecology, Bioinformatics
