Previously, I described the additions that we have made to the kcite plugin [@url:www.russet.org.uk/blog/2012/02/kcite-spreads-its-wings/] which now supports multiple different types of identifiers. This includes the subset of DOIs [@url:www.russet.org.uk/blog/2011/02/the-problem-with-dois/] that come from either CrossRef [@url:www.crossref.org] or DataCite [@url:www.datacite.org] arXiv [@url:arxiv.org/] or Pubmed [@url:www.ncbi.nlm.nih.gov/pubmed/] However, rather embarrasingly, one of the identifiers that we do not support well are URLs. Slightly ironic as one of the purposes behind [@url:www.russet.org.uk/blog/2011/06/ontogenesis-knowledgeblog-lightweight-semantic-publishing/] is to demonstrate that it is possible to replicate the publication experience using the web. The main reason fo…

In my previous article, I discussed my ongoing struggles with DOIs and their metadata [@url:www.russet.org.uk/blog/2012/03/dois-and-content-negotiation/] The article discussed the difficulties with implementing content negotiation for kcite [@url:knowledgeblog.org/kcite-plugin] in particular, getting metadata for a given DOI and understanding that metadata once it had been fetched. Here, I discuss these two issues again! Accessing the Metadata I have previously described the implementation of Content Negotiation for DOIs in Kcite. In the examples given, I used libcurl which has the flexibility to perform content negotiation. One difficulty with this approch is that libcurl is not a standard requirement for Wordpress at least on Ubuntu. So, adding this requirement, forces users to make an a…

With the release of Kcite 1.5 [@url:wordpress.org/extend/plugins/kcite/] we now support multiple forms of citation [@url:www.russet.org.uk/blog/2012/02/kcite-spreads-its-wings/] There have also been some changes to the implementation layer, however, that I will describe in this article. I have previously written critically about DOIs and their problems [@url:www.russet.org.uk/blog/2011/02/the-problem-with-dois/] One of my criticisms is the inability to access metadata about a DOI in a standardised way. In this article, I will consider the addition of content negotiation and whether this improves the situation. From this, I will draw a number of conclusions about the DOI system. Background DOIs offer a single point of entry mechanism for refering to a paper. A DOI such as "10.1371/jour…

Today, I was pleased to release version 1.5 of kcite. Follwing in my tradition of being unable to get the Wordpress plugin release process to work correctly, shortly after I released 1.5.1 which is the same thing, but with the correct metadata. I'm quite pleased with this release. There have been some underlying changes to the technology which I will describe in another post, but for now I want to focus on what I feel represents a substantial improvement on previous versions in terms of functionality. The previous release added support for client-side rendering, which made things look nicer and will add more functionality into the future. However, from an authoring perspective this did not provide much advantage. For the 1.5 release, I wanted to add new forms of identifier. Kcite started w…

We've been working for sometime now on our lightweight semantic publishing environment, kblog. Near the beginning of the last academic year, unfortunately, we were compromised through a zero-day vulnerability. With the press of academic life and teaching, it has taken me a long, long time to get the show back on the road. However, finally, I think we have achieved this. The main cause for the delay was, simply, that I didn't have time --- at other stages of the year, it would not have been so much of a problem, but in October there is very little give in my working week. However, an additional problem has been that restoring kblog was a lot more effort than it should have been. If you are only interested in kblog itself, well, it should be up now. The rest of this post is going to be a tec…

I started to write this post a long time ago in October; unfortunately before I finished I got hit with the start of teaching. I considered just ditching the post, as it is now so out-of-date and I am not usually a zombie poster. However, in this case, I shall post as a) it helps my mind to move back toward research after so long away and b) it will be my first of 2012, so I can check my makefiles work! A couple of follow ups from my previous post. Nicolas Le Novere commented via twitter on even the highest level assertion of that radioactivity is a dependent continuant. @phillord fluorescence and radioactivity are occurrent not continuant. Freeze time to check. @phillord hence the unit of radioactivity: per second (Becquerel) --- Nicolas Le Novere In my original post, I suggested we ne…

Well, I am pleased to say that we have now released the new version of kcite. It's been a while in coming --- I had the difficult bit of the code working about 5 months ago, but then got caught up in teaching. Kcite is our bibliography manager which enables citations such as this one [cite]10.1371/journal.pone.0012258[/cite], using DOI or PubMed IDs. Kcite now uses the marvellous citeproc.js to render the bibliography on the client. The main advantage of this for this release is that the biblography formatting is slightly more regular than before. We've also switched to name-author style as the default. There is also a disadvantage which is that the browser has to do lots of Javascript execution client-side; I've made efforts to ensure that this is not too onerous; on my desktop, I have be…

It has been a long, long time since my last gig review. As this blog is mostly professional now, this is perhaps not such a bad thing. I did half write a review of Roy Harper and Joanna Newsome in Sept last year, but it never got posted. Don't think I have been to gig since then. Still onwards. I've been a fan of June Tabor for a long time, particularly her album with Martin Simpson even if it does have terrible cover art. Despite this, and the fact that she lives pretty close to my home town, I've never seen her live. Her music is dark and eclectic, her voice rich. Combined with the Oysterband's tendency to do strange adaptations folk-style it was destined to be an interesting gig. The music is something like gothic folk if that is not a contradiction in terms. While singing, June Tabor c…

[]{#pici} I once had cause to refer, somewhat mischievously, to "a kind of pasta from Tuscany, which is almost identical to spaghetti, but slightly different"; this was on a mailing list that was used by many Italians. It provoked the expected response; an offended Tuscan responded "I don't know what you are talking about; but if you mean pici", which I did, "it's nothing like spaghetti". Recently, on the OBI mailing list, there has been much discussion about labels, markers or tracers. What ever you wish to call it, the basic idea is the same; a molecule which is easily detectable, is used to trace something else. This can involve adding a small amount of a radioactive isotope (P^32^). This makes it possible to follow the molecule (which is otherwise hard) by…

While I am currently spending a significant amount of my time promoting the idea that blog technology can be, and should be used for serious scientific material, I thought I would make a post of a different and perhaps more traditional vein: that is, a light-weight idea, with no serious research behind it, but Years ago now, I created an Energy Wiki full of daft ideas for making energy. I last revisted this in 2009, with an idea for storing energy at sea. I'd actually forgotten that part of the reason for this was to try out Inkscape, which is part of the reason for this post. I wanted to try a bit of multi-media, that is, a blog post with an image in it. High tech. So, the idea. One form of renewable is the Solar Updraft Tower, also known as a solar chimney. This works straightforwardly e…