Leaving Elba

Elba was a lot of fun; it's very biased toward beaches, but there are plenty of these, they are easy to get to and, generally, free. For my money, the best of these ones that we went to were Aquavivata (or something like that) and Sansone (next to each other --- I swam to the latter) and Capo Bianco. Both of these are withing spitting distance of Portoferraio. which is the biggest town. It turns out that Capo Bianco is part of a marine reserve, which explains, with no fishing; this probably explains why the place was so rich with life that otherwise would have ended up on pasta. But, with a pebble beach, a slow sloping seabed still only 1 or 2m in depth some 50m from shore and with many rocks, and a headland it's ideal for swimming and snorkelling. As well as Elba, I got to Pianosa. This i…

Progressive Inculcation of Language by Listening to Stories

It's been a long time since I posted anything to my Silly Ideas blog. Poking through the source files, it appears that I haven't had a silly idea for a long time, which is a pity. I've decided, however, to create a new category on this blog and move stuff here; the wiki technology is just a little too long in the tooth now. Given that I am on holiday I should, perhaps, stick to lying on the beach and other more traditional holiday pursuits; however, all my silly ideas for the next few years are likely to revolve around variations on the theme of an off-switch for small children; as this isn't very novel, I thought I should take this opportunity while I can. Over the years, the educational demand for second and third language teaching has gone up and up; the world is more international than…

Elba

The last holiday that I went on produced a long stream of blog posts; this one, I suspect will result in only one or two, which reflects the different character of places. India is a place of conflicts, confusion and excitement; Elba, on the other hand, is a holiday resort, universal beautiful, relaxed; in short, wonderful for swimming, sitting on the beach and general relaxation, but not so wonderful for writing about on a blog. I took the train from Rome to Piombino Maritima; as with other times, the Italian trains beat the British equivalent easily. While, in some ways, they are not quite as nice inside, they are plentiful, ontime and cheap; the 15 Euro I paid for a three hour journey would hardly get me past the platform in Britain. Piombino itself, appears to be a scenic chemical fact…

Knowledge Blogging

Some advance on the knowledge blog front this week. Firstly, myself and Simon Cockell spent a short while setting up a development and testing environment and wrote our first wordpress plugin --- "Peaches" based around the Hello Dolly plugin, but with the lyrics from the Stranglers song instead. We finished this yesterday just before automattic released Wordpress 3.0. Hopefully, it will be easy to upgrade. Rather more usefully, I got the very first version of a reference list plugin working. At the moment, it just transforms DOIs into hyperlinks. And, secondly, I got notification from the British Library that they will be archiving the website. Good news, although there are not archives available yet. We move forward!

Northern Rock Cyclone 2010

For the third year in a row, I managed to the Northern Rock cyclone this weekend. It was a lovely occasion as before; the weather was cool in the morning with a brisk wind, but it warmed up a little and the wind dropped by the end of the day. The numbers have gone up slightly and it was good to see so many cyclists around. Compared to last years' ride I was way down. I just cleared 5:30 in the saddle, or 6 hours elapsed, which is about 1 hour slower (although the route is, apparently, 2 miles longer than last year). Not unexpected, given the absence of training; this is my longest ride of the year, 40 miles being the longest otherwise. Having moved house early in the year, and with an F1 in the works, I just haven't found the time. This really is a great event; at the moment, it's big enou…

New Grant for Knowledgeblog

It's been relatively quiet from me for the last few weeks. One of the reasons for this is that I have been submitting a JISC bid. I've not submitted a JISC bid before, so it was quite a lot of work; it's exactly the same as a research council proposal, except for all the bits that differ. The bid, in this case, was for extensions to the Knowledgeblog environment; we want to make sure that it supports research better than at the current time. Our initial experiences were generally good, with a few naysayers. Additionally, we wanted much better linking to external forms of data; array express, Swissprot and the like. And, finally, we wanted to trial this out against a set of specific use cases. Critically, I also got tired of writing "knowledgeblog" the entire time, so they will no…

PhD Position Available

I have a new PhD position available; I am looking to extend some work that I was involved with a while ago now, but into a new area of biology. The idea is that we build an ontological model of the mitochondria, and the knowledge that exists about it. We should be able to build a light-weight model that covers many areas of the biology as an entire system. This will be useful both as an integration point (a traditional use for ontologies), but also so that we can make predictions and search for inconsistencies in the model. In other words, the ontology should be an integral part of the scientific process; we represent a hypothesis ontological and then let the reasoner search for the data for contradictions. This is quite exciting, as we did the original work quite a few years ago, and it l…

The Second Knowledge Blog Meeting

I'm on my way to the second Knowledge Blog meeting. Well, sort of. The first meeting was badged the "Ontogenesis Tutorial" meeting; the focus was on developing a tutorial resource for ontologies. Actually, much the same will be true of this meeting, but I've decided that, for this meeting, as well as addressing the reviews for my own article on Ontogenesis, I am going to want to spend some time supporting the process itself. In the first place, this means writing a couple of articles for Process: a new knowledge blog that I am starting for discussion of the process itself. Since the first meeting, I've had plenty of time to reflect on the general idea of knowledgeblogging. As far as I can see, there is one overwhelming truth about the situation; we got 15 articles in 2 days and, …

Keep the Home Fires Burning

Managed to see "On What a Lovely War" on Friday, at the northern stage. I've not see it before although I've been aware of the play since they did it while I was at school. I guess that being based on World War I, the show starts from an emotional strong point, but the mix of light-hearted and optimistic songs, set against the deaths of millions works as well as it ever did; this version of it was magnificent, with the instrumentation on stage, as props, actors moving backward and forward between playing, singing and acting. Perhaps the most moving section was the 1914 football match in no mans' land, ironic as it has no music over it. The whole play is encapsulated, though, by its version of "Keep the Home Fires Burning" --- the original is a light and jaunty number, a…

Leaving BFO Discuss

Introduction A few weeks ago I unsubscribed from the BFO discuss mailing list. I've been reading and posting there since March 2007; in that time I've managed to send 492 mail messages which surprises even me. As a mailing list, BFO discuss is a slightly bruising experience: it's a bit like a bar fight; one person swings a punch and everyone just piles in. I joined the mailing list because BFO has become somewhat of a force within the bio-ontology community and I wanted to help make sure it was fit for purpose; however, I have to admit that I have been as guilty of reaching for nearest available pool cue as the next ontologist. Not the best side of me, but there you have it. During my time on the mailing list, I have learnt a lot about BFO and the realist philosophy that, in theory, underp…