Always nice to be in Edinburgh, although I'd prefer not to be in a hotel again so soon after ISMB.

Just been to George Hotel: posh, but lots of twiddly bits never impressed me; food was plausible, wine was indifferent, coffee was awful. Staying in the SAS Radisson: good points, free internet; bad points, they have authentic wooden windows to look nice, and a inner draw window which acts as, well, a window. Sounds fine, but it's single, transparent sheet of glass, 10cm in front of the wooden frame and I nearly broke my nose on it trying to look out of the window.

Ouch.

p.s. there's a 2cm step between bedroom and bathroom with no function other than to provide a place to stub your toe.

So, I am sure the world is waiting to know what I thought of it; actually, it's very good. Although it is long, it does not feel flabby like the last book. It is by far the darkest of the books, with familiar object and characters dying off left, right and centre — it's clear that she does not want to leave any possibility of a follow up. The plot is fast and thick. As previously, she starts fast, then slows for the middle, then speeds up again. I though that she managed to tie up all the loose ends rather well, with her rapid style mostly covering up the technobabble (or whatever the magical equivalent is).

I'm glad she's managed to pull it off. With the combination of Harry Potter and Northern Lights, we seen two epic serials released. I am sure that they will be read for many generations to come, but only we will be lucky enough to have had the anticipation of waiting for the new books as they arrive.

Spent today walking around the Prata, out as far as the stadium, then back to Lassallestraße. The day was clear, perhaps slightly too warm, but really nice despite this. Good to spend time relaxing before the flight.

Vienna airport needs to get it's signs sorted out though. The restrictions all state that you can items bought on the transit can be taken on the planes, but then they put security other side. It's not a surprise really that people get annoyed with these restrictions when their signs are wrong. Now I have to fly without water. Hopefully, I won't get ill.

Having been in Vienna for a week, I thought I would comment on the food. In general, it's very good. I can't point my finger at a single bad meal (although several inappropriate ones — more later). The most common kind of food that I eat was Italian. As a world cuisine, it has the advantage of being the least offensive to all concerned. Both resturants that we tried were good; one of them managed to achieve a feet that I would have not believed possible and cooked a meal which might just have had too much garlic (gnocchi in garlic, chilli and olive oil). I eat Austrian food twice. One resturant mostly served boiled cow; here, I had Chanterelle mushrooms in white sauce which were nice, although the meal needed more variation. The other was for the conference dinner — queues were long, everything was meat, with the exception of fried, battered vegetables. The wine was not very good either. I think beer would have worked better for a meal consisting largely of bones. In general, conference meals were good though, although occasionally dull. The salads were really nice, although they kept running out. I guess the Viennese eat these as garnish, and served them in quantities appropriate for this.

The two highlights, though, were the the bakeries. I had croissant and coffee everyday. The coffee was rich, strong and without bitterness, while the croissants were delicious. The only exception here were the two breakfasts I had in the Ibis Hotel where I was staying; the croissant were stale and tasteless. And, finally, last night we found a Japanese. Not the greatest I've ever been too, but it hit the spot. The food was pleantiful, cheap and well cooked. I ended up having a second main meal, although we split it between two of us.

Been to a number of tourist traps over the last few days, so here are my opinions.

Zoo: well, lots of sad animals in small cages. They should shut this, move it 20 miles outside town, run a shuttle bus and give the animals more space.

Palm and Cactus House: there were really good and fun to walk around. Smaller than either Edinburgh or Kew, but still good.

State Opera House: it's okay. It is basically a confusing mix of styles, with lots of twiddly bits on. In the end, we only went there because of the rain, so I can't really complain.

Finally, ISMB is coming to an end. The database and ontologies track had a couple of interesting talks, with Suzi Lewis' being the day before. To finish off, I am in a Open Science meeting — rather smaller than I thought it would be, but this might be because it was not very well attended, but then it's at the end of the conference.

Not a bad conference, but too long as always.

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.

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 — mapping between one resource and another: in this case MESH and Swissprot — to support the flow of knowledge from bioinformatics research toward medical practice.

10:10

The mapping theme continued (you'd almost think it was planned!) by Julie Chabalier who has mapped a number of resources to build a query warehouse.

11:00

Judy Blake has just spoke on annotation of GO and exactly what they mean. It's good to see an increased formality to the relationships between a GO term and the entity that it is describing. This talk has generated the most questions so far, mostly asking for more details.

11:29

Mikel Arungen is now talking about design patterns, which are analogous to software design patterns. These should help to bridge the gap between the desire to write rigourous logical definitions, but the difficulties of doing this.

11:51

Daniel Schober is now describing efforts to standardise naming conventions, fitting with the theme of methods to help people produce interoperable and standardised ontologies.

12:10

Lunch, and nearly on time. Most of the lag was from coffee break, so I don't feel that I, as timekeeper can be held responsible for this! Next for poster session, followed by the panel.

14:00

Well, the panel session has an element of self-indulgence about it. Robert has been doing this for much longer than I, but even for me it's four years. After such a long span, it'a amasing that we have got to ten yeas. All of the speakers commented on how big the community has got, and that we are all a little surprised about this. The current religious themes running through bio-ontologies are also here, but so far fairly muted. A good panel all in all, and a nice marker for 10 years.

16:00 (ish)

Larisa Soldatova's talk addressed the need for an tool enabling scientists to add additional semantics to their written work.

16:30

Catia Pesquita is talking about semantic similarity, which is a topic close to my heart. An interesting and careful body of work which covered the ground well, I thought.

16:50

Kieran O'Neil is not showing some interesting research, where he has been investigating novel techniques for query building over integrated databases.

17:10

Irena Spasic talked about some building term lists for metabolomics from literature mining. Once again she highlighted the need for access to full papers.

17:30

Daniel Faria took the graveyard slot, and discussed measure for protein clustering using sequence and GO information.

Conclusions

Overall a good day. It was great to have some many papers, and such a lively debate. This also marks the retirement of Robert as co-chair. His presence will be greatly missed — he's taught my everything I know about being relaxed and not faffing too much while conference organising.

Onward till next year.

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 named after Frederich Lassalle, but it has little, potted life histories on the road signs. At least, I presume thats what they are. It could say "Frederich had a big nose, bad temper and we are glad that he is gone".

Now that the temperature has reached over 20C, I am tempted to be British and lie in a air conned room, sweating and moaning. I think, however, I shall pop out and do the inner ring. I wish my sandles had arrived with me; I fear this evening I shall need surgical separation from my socks.

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.

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.

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 to Gnus, but that is it. Gnus uses an one message per file, text based format. It's pretty future proof; I suspect in 2000 years, when people look back they will assume that everyone used Gnus and similar applications, as all the PST files will be unreadable. There's a big gap in the middle of my email for 6 months after I got to Newcastle, when I had used Outlook. A pity.

My total collection of email is 1.4G in size — I've been reasonably careful about dumping 100M attachments over the years. The earliest email sent by me talking about SET domains in a Drosophila gene. The oldest email I can find sent to me comes from 1994. It's from a nice bloke I remember meeting on one of the guitar boards, called Paul R. Leach. At that time he was at Colorado. He was kind enough to send me some Herco Flex 50s from the US. These are guitar plectrums that seem to have disappeared from the market at the time. I think I still have a few of them left. Thanks Paul! An act of generosity, that I now remember 13 years later. The internet was a kinder place in those days.

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.

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 can't comment.

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 future. It's notable, that I have 15 year old latex documents on my machine and on the whole they still just work; when they do not, almost all of the knowledge in them is easily recoverable with a text editor. As far as I can see, the only way that you can guarentee that a file format will be usable into the future is to make it as simple as possible.