Yesterday was the SIG co-ordinators meeting for ISMB. One of the big and recurrent issues (besides the timing of coffee breaks) was the timing of ISMB. At 7 days, ISMB is a long, long conference and is a bit of a killer. Of course, bringing it down to 4 days will mean that more events will run concurrently. Live with it, I say. Bio-Ontologies was a success, but I want to think about the future (Blair-like, perhaps I am thinking of my legacy, as I will not chair it for that much longer). Perhaps, "Bio-Ontologies: knowledge in biology" would be a way to go — I want to move the workshop away from a technology and more toward a function. Originally published on my old blog site.

10th Annual Bio-Ontologies Meeting

Today is the day of the Bio-Ontologies SIG meeting, which I have now co-organised for 4 years or so. It’s a surprisingly large amount of work to do, not least this year because we had 36 submissions. The organisation of this is a large part of the effort, but it has made for a strong programme; it’s gratifying to see that we have an audience of size to match. 09:10 We had a moment of worry when the first speaker didn’t register, but Mark Musen is a notable replacement, talking about representing OBO to OWL mappings. 09:30 Following Mark’s talk about using more rigourous models of OWL, Simon Jupp is talking about using the more light-weight semantics of SKOS, which turns out to be well suited for document navigation. 09:50 Lina Yip covers a familar problem &mdash…

Vienna by day

My initial impressions that Vienna is not 24hr were confirmed today. Wandering around the shops at 9:30, I was greeted with looks of amazement that I should want to buy anything at such an ungodly hour. I found the electrical cord I needed, and some sun tan cream; the chemist shop was small and prissy, with signs for "laxa soft" everywhere; mute testimony that Viennese food is Germanic — everything you can decently do with a sausage. The city itself is not, to my mind, beautiful everywhere as the taxi driver suggested, rather it is impressive. The buildings are large blocks, heavily ornamented and shine in the sun. The streets are wide and gentle, with a confusing combination of foot, bike, tram and car lanes. The street I am on — Lassallestraße — is not only…

Vienna by night

I’ve just got to Vienna. I got here at some stupid time, but I had time to pop out and see the Prater. There’s an currently a film festival on, and there were showing an outdoor film — sadly I’ve missed Dr Strangelove. I recognised the ferris wheel from another film, Before Sunrise. So far, seems like a nice city to me, although around here at least it’s clearly not a 24hr city as everything was switching off. Anyway, I won’t say more. I got here fine, but my luggage is in Paris as is my power adaptor. Better hit the electrical store tomorrow. Originally published on my old blog site.

Mouth of the Tyne Festival

The Mouth of the Tyne festival was excellent as always. I didn’t get to see as much of it as I wanted, but I saw some great Blues (Stax Brothers), an excellent French jazz band who were fabulous, the Blockheads who were stonking. Finally, I got to see Courtney Pine again — I’ve managed to miss him for the last 15 years, so it was particularly irritating that the rain made me miss some of this. Originally published on my old blog site.

Preservation for the Future

I’ve been attacking email systems this week. I’ve been helping to transfer email from the Nottingham exchange server upto Newcastle. The process has not gone easily. I think that the problem is that university IT departments think mostly about their current users, rather than users coming or going elsewhere. To me this is a real problem: for an academic, their correspondence is an essential ingredient of the historical record, their knowledge of what they have done. Spurred on by this, I decided to recover all of my mail from the archives where I have kept it, and place it into my current email system. This is made easier for me because I have used Emacs for pretty much my entire time on a computer; I remember a DOS based application before that. I’ve moved from RMAIL …


Tried to install Feisty recently. Turned out to work fine (the proxy business at install now works). But there were still problems. The mouse configuration (I use a logitech marble mouse) was a pain. Logitech make nice equipment but their devices never work properly with anything else and are hell to configure. Combine this with Xorgs bizarre configuration scripts (while they have sadly not thrown away since the fork). I find it incredible that no one has written a nice mouse configurator, and more incredible that you have to restart X to see what the effects are. This really needs to be sorted. Originally published on my old blog site.


Blackfriars is a very posh resturant in Newcastle. I’ve been there a couple of times, and the food is reasonably good. On monday, I eat there; the veggie option is small but looked reasonable. I went for the stuffed aubergine in the end. It came with breadcrumbs and ratatouille (that is the contents of the aubergine cooked in tomato), rather than the cous cous that was on the menu; a pity as it happens, as the whole thing was rather too dry; something that would probably not have affected the cous cous. In general, it’s confirmed my opinion. Blackfrairs is okay, but when you get down to it a polysyllabic menu, and artful arrangement on the plate does not make up for the unspiried dishes and a lack of flair for vegetarian food by the chef. Course, the meat might be great. I c…

Aging File Formats

An interesting article on the BBC today about digitial preservation. The issue is a well-known one, that file formats go out of date very quickly. They have a chap from Microsoft showing that you using a virtual machine you can still open word 3.0 documents; this seems to miss the point, to my mind. Great, so I can still read it, with my eyes, by looking at it. But can I compute over it? If we are to take this approach, then it might make more sense to just print out over thing that we want to store and save the paper. I think that it’s good that we are moving toward open documentation standards. Microsoft’s standardisation of their file formats is welcome, if belated. However, it has to be acknowledged that a large, 6000 page specification is going to be a problem in the fu…

Into Great Silence

Went to see Into Great Silence last night. It’s a film about a bunch of monks who don’t talk much; so the entire film is meant to engender a feeling for the contemplative life. The filmmaker has gone to lots of effort to make it peaceful and relaxing, while not too dull. He uses lots of wacky angles, film, video, even super 8 by the look of things. On the whole, it worked well; only a few people left, although someone just behind snored through half an hour of it. I thought it was overlong at over 2 hours. I was rather moved by the serenity of the monks, by their enormous sense of peace; they were also deeply worrying. There are only a few pieces of dialogue: one was a reading which was rather rambling gibberish about the trinity; the other was a interview (although the film…