The ability to create PDFs for the articles BioStor extracts from the Biodiversity Heritage Library has been the single most requested feature for BioStor. I've taken a while to get around to this -- for a bunch of reasons -- but I've finally added it today.

The TreeBASE team have announced that TreeBASE II has been released. I've put part of the announcement on the SSB web site. Given that TreeBASE and I have history, I think it best to keep quiet and see what others think before blogging about it in detail. Plus, there's a lot of new features to explore. Take it for a spin and see what you think.

Yesterday I fired off a stream of tweets, starting with:Various people commented on this, either on twitter or in emails, e.g.:So, to clarify, I'm not abandoning wikis. I'm just frustrated with the limitations of Semantic Mediawiki (SMW). Now, SMW is a great piece of software with some cool features.

This post is simply a quick note on some experiments with DjVu that I haven't finished. Much of BHL's content is available as DjVu files, which contain both the scanned images and OCR text, complete with co-ordinates of each piece of text. This means that it would, in principle, be trivial to lay out the bounding boxes of each text element on a web page.

Continuing the theme of ancient programs of mine still being used, I've been getting reports that the Windows version of TreeView won't install on Windows Vista and Windows 7. As with NDE, it's the installer that seems to be causing the problem.

Chris Freeland tweeted about the presentation he gave to a recent BHL meeting, the slides for which are reproduced below: BHL Tech Report View more presentations from chrisfreeland.It makes interesting viewing. From my own (highly biased) perspective slide 10 is especially interesting, in that BioStor, my tool for locating articles in BHL is the 8th largest source of traffic for BHL - 2.46% of visitors to BHL come via BioStor.

It's Friday, so time for either a folly or a rant. BHL have put another user survey into the field http://www.surveymonkey.com/s/BHLsurvey. I loathe user surveys.

I've made some progress on a wiki of phylogenies. Still much to do, but here are some samples of what I'm trying to do.First up, here's an example of a publication http://iphylo.org/treebase/Doi:10.1016/j.ympev.2008.02.021:In addition to basic bibiographic details we have links to GenBank sequences and a phylogeny. The sequences are georeferenced, which enables us to generate a map.

I'm revisiting the idea of building a wiki of phylogenies using Semantic Mediawiki. One problem with a project like this is that it can rapidly explode.

A little while ago I came across Wikisource, and it dawned on me that this is a model for BHL. To quote from the Wikisource web site:Much of their content comes from the Internet Archive (as does BHL's), and Wikisource have developed extensions for Mediaiwki to do some cool things, such as extract text and images from DjVu files.

I've written up some thoughts on Wikipedia for a short invited review to appear (pending review) in Organisms, Environment, and Diversity (ISSN 1439-6092). The manuscript, entitled "Wikipedia as an encyclopaedia of life" is available as a preprint from Nature Precedings (hdl:10101/npre.2010.4242.1). The opening paragraph is:The content will be familiar to readers of this blog, although the essay is perhaps a slightly more sober assessment