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.

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.

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.

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.

As one person said of my blog, it’s a bit weird, what with you thinking you’re still in India. It’s been a long time now, that we’ve been back, and I’ve had a lot of time to reflect on the experience. Writing the blog has served it’s purpose though; since I’ve been back, I’ve marked exams, taught two modules, run a meeting and submitted a paper. The holiday seems a long time ago, but the notes I took for the blog has helped me to remember the experience; for this reason, even though I wrote most of these reflections while travelling, I’ve decided to write these from the present, as opposed to the past present tense all the other posts have used.