It's the end of the world as we know it

Yes, I have decided to finally put an end to this blog. No more exciting posts. No more rants. No more daft ideas.

Not to worry, I have moved it to a new location as from today. This site will remain active, well, forever as far as I am concerned, but no new updates. The content has been transferred, although comments will stay here only. Hope to see you all at the new window.


DCC/RIN data management workshop

Just coming back from this Digitial Curation Centre/RIN data mangement workshop. It was an interesting meeting with lots of discussions; I know relatively few people there, so it was a new environment for me. A lot of it was about establishing value for data sharing — something which is hard to do because, by definition, there is a time lag between the lodging of data and the point at which it actually gets used.

One of the problems with establishing value was that the talks seemed to cover two different types of repository; for example, Matthew Wollard for the UK Data Archive really is maintaining a data archive. The datasets there are curated for metadata, but other than that, it's the raw dataset. On the other hand, most of the value that Jenny Walsby of the British Geological Survey talked about was from "value-added", secondary analysis of their primary data sources; for example, rather the releasing raw data about the presence of clay soils, for the insurance companies, they release risk factors for subsidence. Likewise, for biology most of our database "curators" are actually annotaters; they add more to the data than it started off with.

I found a couple of the talks slightly concerning; Simon Hodgson from JISC was talking about institutional repositories; something I have ranted about before. From questions afterward, he is clearly not limiting the proposed support to single institutions which is good thing; structuring knowledge along the lines of the current financial and managerial organisation of the universities, rather than along the lines of, well, something sensible and comprehensible does not seem a good idea to me. Secondly, Adam Farquar of the British Library gave a detailed talk about their plans for DOIs for data. I think that the social aspect — that data should be a first-class citizen with papers is a good idea; well, sort of; actually, I think we should value data and not the current publication proces, but that's a slightly different argument. I'm not convinced by DOIs though; technologically, DOIs are handles, with some social conventions layered on top for the publishing industry. The technology is good, but the social conventions are just wrong for data; an individual may want to release thousands of datasets a day, rather than 100 papers a career; they may want multiple versions or refer to subsets. Getting this to work with DOIs doesn't make any sense because you have to fight the social conventions; why not just use handles directly; this side-steps many of the issues (like the cost to DOIs, and the bias in the registration process to large organisations), while still building on the mature infrastructure base (Handles) that makes DOIs successful.

After all, Nature Preceedings did this for preprints; I suspect most people don't even know that they are not using DOIs.

One issue which also came up was identifiers; a pet topic of mine. In this case, identifiers for indiviual scientists. PLoS recently commented on this (I'm a number not a name, I think the title was — am on a Cross Country train, so can't check) also. It's about time, we got this sorted out and it's much more tractable than most identification issues in biology. I have some ideas about this, which I may blog about in a few days time.


Waiting for Godot, Show of Hands, Swing out Sister

Been to so much recently, that I've hardly had time to keep up.

Waiting for Godot was on at to Royal Theatre. Looks impressive but is not a good venue. The acoustics are bad and the seats are uncomfortable. Still, it was Ian McCellan and Patrict Stewart on one bill, with Simon Callow and Ronald Pickup thrown in for good measure. What can I say, really. The cast made the occasion. The play was funny and engaging, even if it makes no sense. The set was wonderful. Seeing Mr X and Magneto at the same time, though, what more could you want? Well, apart from comfortable seats, that is.

Show of Hands. Yep, great. Barn storming, folkie-inspired, throw some politics in. They really filled the hall (Sage one which is famously hard to fill, being cold and antiseptic). Heard about them many times before, but as it happens, never seen them or heard any of their stuff. Good introduction, this was.

Swing Out Sister, finally — not my choice, not really my sort of thing, but I am a music junkie, and always willing to try anything. Besides which, they were fun in the 80s and compared to SAW were a relief. Live, they were great. The music is upbeat, engaging, entertaining. The band were fluent and the night really, erm, swung. They started off with two of their big hits (Surrender and another one I forgot the name of) which seemed curious; as well as these, they had a few stand-out songs, although even on the more pedestrian numbers, it was all very listenable and enjoyable. The encore was the inevitable Breakout — "when you've found a good thing make it last" — Swing Out Sister seem to have done this, and I'm glad.


iPlayer still rubbish

Today, iplayer tells me "You have download 2.22 of content" with a checkbox saying "Do not show this message". Robbed of a unit the former looks messy, robbed of "again" the latter looks a bit "Do not press this button again".

Download times have come down a bit. Still — 4 hours now for a 60 min programme. I even managed to get something to play today; the frame rate appeared to be about 5/second.


Web 2.0

What a flurry of posts? I went mad today and joined twitter and friendfeed both at the same time. Gosh, what a time waster this stuff all is.

Right, just got to twitter about posting on my blog.


iPlayer Update

Managed to download a file; it doesn't block so badly at 5pm. Can't get the file to play in any way, shape or form. There is, however, a solution. What you do is click on the "download to windows media player" link. This gives you a straight forward URL from which you can http download. This is actually better, in many ways. You can use what ever download manager you like, including a vaguely capable one. You don't have to guess which file is which as you did before. And as soon as some one has worked out how to pull the URLs out of the BBC's UI, we should be able to circumvent the entire process of going to their website.

So, perhaps it's not all doom and gloom after all.


BBC iPlayer Desktop

Just been forced to "upgrade" to this, despite having no desire to. It's very impressive. It will only do a single download at a time and is current reporting 10 hours left for a 1 hour programme; the old BBC IPlayer would download in about real-time, certainly after 10pm in the evening. I did manage to download one programme in 5 mins, but sadly the file was only 32k at the end and it wouldn't play; really, really broken. And, of course, it's ditched my existing programmes despite promising to keep them.

Apparently, they have ditched P2P for IPlayer Desktop; good idea, if you ask me. Lower CPU load, no upload traffic generally good. But you have to upgrade your servers, guys. And, of course, the entire internet, to avoid the slowest link effect. Very poor indeed. The message boards would be floods of moans; lucky that the BBC had the foresight to close them down.

Ironically, they've gone high definition; it was announced on the website. Great idea; a week to download 5 mins, but looks great when you do.

Very poor; has to go down in history as one of the worst damn squib launches I've known. I wish I knew how to upgrade back to the old iplayer.



Did the update. RC1 is out which is a reasonable time. If I updated on the release day it would have taken for ever; last time, it took something like 2 hours. This time the whole process was over and done with in an hour. It's all been relatively painless. So far only two problems. Obviously my marble mouse configuration stopped working again, and I had to change all my HAL scripts; luckily, this is now better documented than before. A great relief because following through the myriad pieces of advice on how to do this every update was getting taxing. And, secondly, they've introduced something called "screen-profiles" which is colour schemes for screen; very nice, I'm sure, but when it seems to be kicked off when I start screen with an aliases, asking me lots of questions. Uninstalled it; problem gone.

And Jaunty? Well, it looks nice enough. Boot time is definately faster, although my windows box still beats Ubuntu (there is less on it, to be fair). Login screen looks very cool. Other than that, well, all ahead as normal.


Emacs and Blogs

People seem to be talking about my post on upper ontologies. Half of them are moaning about my blog software.

Look, the point is that the user interface is nice and simple for me. I just type stuff into a text editor, I can do it offline and it all works. No one else needs to use it if they don't want to!

Of course, it would be good to use something better, but not if I have to fiddle with any of the 100s of rubbish online editors that I've seen. And it's too hard to change now.

Bah, humbug.


Functioning in the Upper Reaches of Knowledge

When Peter Murray-Rust restarted blogging recently, I must admit that to having mixed feelings. His blog is very interesting, often insightful and entertaining. He is, however, rather prolific, making up a considerable chunk of my RSS inbox. This would be okay if he was dull, of course, as I'd just unsubscribe, but it's not true.

As a case in point, he recently talked about Ontological Wars; this lead me to the Upper Ontology page on wikipedia which I'd not read before. Mostly of this page is not about upper ontologies but two sides sniping at each other about why upper ontologies are or are not possible.

Since the whole idea of upper ontologies came into bio-ontologies, I have to admit to being deeply ambivalent about them; I can see the appeal, of course. There is a pleasure at fiddling about at the upper, most abstract levels of knowledge. Career-wise, upper ontologies are high-risk but think about the potential publication rate if every one uses your ontology; of course, the actual value might be small to each individual, but if you get a publication out of each; well, it's like writing Maniatis (famous for having a funky name, as well as the book), or BLAST (which gets cited by everyone).

The flip side is that, I think that there is rather little evidence that using a single common upper ontology actually aids the processes of ontology development, deployment or integration. It can help somewhat, but then people end up spend too much time thinking about the philosophy of upper ontologies, which ultimately can take a lot of time; take a look at the BFO mailing list if you want to see how I have fallen in to this trap. On the other end of the process, how much use is an upper ontology in terms of querying? For example, it might be good to know that the function of a test tube and the function of beta-galactosidase are actually instances of the same RealizableEntity, but does anyone ever query at this level of abstraction.

I think that the core problem here, is that upper ontologies tend to be built without evidence; rather illustrative examples are chosen and then used to derive general truths. An illustrative example of this approach is, for example, Barry Smith's paper on part of; the example is a circle half of which is red, half of which is white. Okay, but where is the evidence that this is a good example? Can we be sure that if we picked a different example, the conclusions would not have been different?

This, I think, covers the key problem. At the moment, are attempting to build upper ontologies from the top down; those people who are interested in upper ontologies tend not to apply them to large scale projects; those people building lower ontologies tend not to discuss the applicability of upper ontologies for fear of getting shot down in flames; see wikipedia if you like flame wars. What we need is an arbiter, some way of determining who is right, who is wrong; as a scientist, of course, I know how to do this; I do an experiment. You can argue philosophy all you like, but having not one illustrative example can never outdo having several hundred actual uses. We don't entirely know how to do these experiments yet, but that's partly because we are not trying. I once got told on the BFO mailing list (and I paraphrase): YOU can do controlled experiments if you like, but I'm too busy doing science for that.

In ontology building, we need to avoid arguments like "is it correct", "is it true" or "is it reality" and replace them with "does it work". And to do this, we need to take a small step back and ask: how do we know when our ontology works; and most importantly of all, how can we guess when its likely to work in the future. Only then can we choose with knowledge between the different upper ontologies or, indeed, none at all.

Enough philosophical ramblings; back to work.


Cygwin Problems

I've been getting recurrent problems with the ssh service on cygwin. It was crashing with a wierd fork, malloc style error that I just had no chance of debugging. It's been causing me real grief. sshfs has stopped working, unison has had problems. But it's only been intermittent, so I never got around to fixing it.

Today, I did the google thing. And the cause? Think hard, have a guess, I promise you will be surprised.

My web cam drivers. Of course, I hid the critical information from you — I have attached a device from Logitech to my machine; I've ranted about logitech before, but this one takes the biscuit. They really do make some of the worse software known to man. I mean, how are you supposed to figure this one out? Hmmm, a key component of my secure networking is causing problems; what can it be? Perhaps, it's my webcam software.

Uninstalled their QuickCam disaster. The webcam still works. So far, no ssh problems at all.


Consortium Meeting

Well, just had two days of a Carmen consortium meeting. Very interesting to see how things have changed as time goes on. Also, two days of University food with a stop of at "Louis" last night; the latter is in Jesmond, so as you might guess the restaurant was affected and effete. You could tell that it was very high quality, though; they used big white plates, with the food in the middle and a sauce drissled around the outside. It's good to eat such high quality food even if, as in the case, it doesn't taste that great. The soup was vegetables lightly boiled in a weak broth, while the aubergine lacked only aubergine. The University food, on the other hand was, well, University food; lunch today consisted of potato in several forms.

Tonight I had some bread, humous and a salad, with sweetcorn to start. Ah!



I used to listen to the Chumbas lots. They bestrode the 80's and the 90's particularly as a live band; they were constants on the festival scene. They consistently produced wonderful pop records, danceable and wonderful, underpinned with an anarcist heart and strong political message which always seemed at a counterpoint to their lightness of their sound.

Unfortunately, I was really busy in the 90's and never saw them live, which was a pity; so I was a bit surprised when they turned up in the SAGE programme; why not, I thought.

Turns out, in the mean time, they have transmogrified into a 4-piece acoustic folk band; the harmony and lyricism of "homophobia" has ceased to be a standout and become their mainstay. As in the past, they retain their ear for catchy tunes, a strong sense of humour and lots of politics thrown in. The acoustic band seems here to stay; an 8 member electric bank is just too expensive in this day and age.

I'm kind of sad to have missed them in the first incarnation; but I'm really glad to have seem them in their second. They were wonderful and I enjoyed every minute, even if I could have done with a bit of dancing.


Elliot Brood

Turns out that I have not actually been inside the Tyne pub before, although I walk or ride past it more or less everyday. Nice place inside; has a slightly mid-west US feel, with a long bar, high stools and a Budwieser neon sign. Fortunately, the beer bears little resemblence to the US counter-part, and they've put coat hooks under the bar, which means your jacket doesn't great trambled when it falls of the back of your chair.

There were 3 support acts on; all three were pretty poor at promoting themselves and I didn't pick up the names, although the last one sounded improbably like "The Courgette Sisters". First, up where man, woman, two guitars, nice songs. Fluent and organised, there were fairly good, although perhaps moving toward the inoffensive end of things. Second, were a strange four piece who mixed flamenco, blues and folk; sometimes successfully, sometimes less so. When they got going, though, they banged out a fair rhythm. If they can get over the occasional tendency toward complexity for the sake of it, they will be great. Finally, the aforementioned Sisters. Good stuff, nice voices, but they didn't dazzle me.

The main act, Elliot Brood, have been billed as Death Country. Actually, this pretty much covers it; the songs are country inspired, all acoustic instruments, but then with fuzz on top. Add in the occasional metal chord change and you have it. Pretty good as it happens, lots of opportunity for headbanging and general dancing around even if, by this stage, I was falling asleep in my beer. It was helped by the atmosphere; quite a few Canadians who were probably a bit surprised to find their band playing over here in a small pub. Often the best kind of gigs these.



A few days ago my todo list was empty. Today I have my window open because my office was getting a bit stuffy. Spring is here! Wey Hey!


I hate latex

I just spent 40 minutes trying to get the Bioinformatics class files working under linux. Pain in the ass. The problem is that Ubuntu has moved from teTeX to TeXLive, so things are all different. Canonical have also screwed around with TeXLive and teTeX a little also, so that they can install either; hence you have /usr/share/texmf-texlive rather than /usr/share/texmf. Under no circumstances could I get it to work; it just would not recognise the class file.

I tried:

  • adding it to ~/documents/tex which is my TEXINPUTS. This is my usual technique. Didn't work.
  • Adding it to ~/texmf which is, apparently, the recommended technique. Didn't work.
  • Adding it to /usr/share/texmf-texlive and running texhash and makelsr. Didn't work.
  • Adding it to /var/tex. Didn't work.
  • Adding it to the same directory as the .tex file. Didn't work.
  • Swearing a lot. Didn't work. Didn't even make me feel better.

LaTeX really irritates me at time; the problem, is been around so long, and much of the documentation that you find on the web is woefully out-of-date. The lack of debugging statements don't help. It's really hard. Sometimes, you feel it must have been written by a bunch of idiots.

After 40 minutes, I fixed it. The file is bioinfo.cls, not bioinf.cls.



My todo list is empty.

Really! Empty! I mean, like, with nothing in it, with nothing immediate, no heavy deadlines hanging over my head. Tomorrow I can do something fun, like some research or think of something new. Wey, Hey.

I'm going home to eat pancakes.


Relative Risk

I'm kind of irritated by the response to David Nutt's comments on Ecstasy and horse riding. He's been widely slated by various politicians, desperate to get their "tough on drugs" soundbites.

"There's no comparison", said one. "Horse riding teaches you discipline", he said, making a comparison. Well, yes, maybe it does. But it also rather likely to kill, cripple or maim you.

It's not an issue of choice, of opinion, whether horse riding and ecstasy are as dangerous as each other, it's an issue of evidence, and measurement. We can, potentially, answer the question. What we choose to do about it is a different issue, but, having measured the risk, to argue against ecstacy on the basis of danger is a poor argument if there are many other equivalent activities.


Grace Jones, Richard Thompson and Arlo Gutherie

Grace Jones wasn't my choice but I thought "what the hell" and went anyway. We were sitting up in the Gods close to the stage but vertically way above it; odd, but I quite like these seats; they are quirky and strange in the otherwise antiseptic, boring Sage hall one. She put on an amazing performance; the musicians were wonderful, accurate and precise, totally co-ordinated. Watching the choreography of the show was incredible. The stage had been marked up and organised with gaffa tape, everything in it's place; even the exit route for the "spontaneous" stage invasion was carefully marked out and free of wires. At the end of ever song, she rushed off stage to the dying chords, changed costumes, while keeping up some off-stage audience banter. And the music? Started off quite funky, got more rock as we went through. I only recognised a few songs including a strange version of Love is the Drug (with a clever laser effect, shining down onto her sparkly hat, like a wearable mirror ball). The grand finale was Slave to the Rhythm sung while rotating a hula hoop.

Richard Thompson was, as always, wonderful but the total opposite. Three people on stage, with a projected backdrop; wonderful guitar playing, lots of humour in between. He was playing "1000 years of music", taking songs from, well, the last 1000 years, skipping over centuries at a time in the first half. The second half went decade at a time. A great night of music, I thought.

Last night was Arlo Gutherie, in Durham. I've not been to the Gala before, but it was a welcome change from Sage (where wouldn't be). It's a small, discrete theatre, but warm and welcoming inside. The show started with the somewhat strange "Landermason": I quite enjoyed them; they were technically adept (perhaps too much) and their arrangements were novel and quite interested. That said, one of my friends, Gerry, described them as "absolutely awful". A bit harsh perhaps. Arlo, on the other hand, just came on stage, played guitar and told stories. He played and spoke with the fluency of someone who has been on stage all his life, the songs were straight-forward, honest and moving. The stories in between were very, very funny and often took us back through the 20th century, talking about figures who have become mythological in some ways now but who were just guys travelling around the US, singing songs, trying to make ends meet.

Outside the theatre, it was a normal friday night in Durham, lots of people walking around, slightly drunk. There was a woman busking outside, playing Wonderwall on an acoustic with a small amp; seemed appropriate somehow.


Farewell, John Martyn

Just read the news that John Martyn has died, so soon after I last saw him. Not a surprise, as he hasn't been well for years. I've seen him so many times over, though, and will miss his music immensely; recorded he was great, live he was incredible.


Daft Error Message of the Day

"Dr Watson Postmortem Debugger has encountered a problem and needs to close. We are sorry for the inconvenience"

The pulseaudio problem described earlier wasn't. I managed to uninstall pulseaudio and Ubuntu is still crashing. Eech, this is not good.


New Times

The installation of a new US president is always an interesting time. With Obama, I feel rather torn. Having a black president is not an achievement as such, rather (a sign of) the ending of lack of achievement (for the country, of course; for Obama it's a huge achievement). My general cynicism about politics makes me ask the question, who is he going to bomb then?

On the flip side, I don't feel the enormous sense of disquiet that I did on hearing that George W. Bush had got elected for the first time. Nor the sense of resigned depression on the second election. We don't know how Obama is going to turn out, whether his fine words will turn into fine actions. But, at least, we are not where we were with Bush; where his stumbling words would only turn into fine actions if it happened by chance.

Did I just say "things can only get better"?



Why the hell do people insist on sending "please remove me" mail messages to mailing lists? I mean, if they are on a mailing list that they don't want to be on, have they considered the possibility that other people are in the same boat.

This has happened to me twice today, once on a local UCU mailing list and, once, on a conference mailing list.

Roll on universal identifiers for scientists. We can use them for blacklisting. Anyone sending a "please remove me" mail message will be right up my list, I can tell you.

Ah, that feels better.



The maddness of Linux sound continues to plaque me. Pulseaudio is crashing Gnome on an hourly basis. It get an obscure message like this in my /var/log/messages.

pulseaudio[14900]: pid.c: Stale PID file, overwriting.
pulseaudio[14900]: main.c: setrlimit(RLIMIT_NICE, (31, 31)) failed: Operation not permitted
pulseaudio[14900]: main.c: setrlimit(RLIMIT_RTPRIO, (9, 9)) failed: Operation not permitted

I've tried adding myself to the pulse-rt group on the basis of a 2 year old message about Hardy, and setting ALSA manually in the sound options. Eeech, this is not good. Haven't had this level of instability since, erm, RedHat 5.

I tried removing pulseaudio entirely. Sadly, Ubuntu-desktop depends on it. So, removing it would fix the crashes but in a way which, I feel, rather defeats the point.


Where Pedro has gone

Previously, I asked where Pedro had gone. Well, I'm delighted (although mystified) to find that he seems to have actually read my blog, because he's left a comment on it.

I'm not quite sure why I had such troubles finding him on Google — possibly a bad day; I think mostly it was just that his website doesn't mention Pedro's tools anymore. He's been building CAZy, which I know of, although I don't think I've used it. Poking through his bibliography, he's published on semantic similarity, one of my pet topics.

It's amazing to me how much traction Pedro's tools has got with bioinformaticians/biologists; during the Ontogenesis at which I was present last night, I mentioned the website and the three who were old enough all perked up, saying "yeah, Pedro's tools was excellent". We started comparing Pedro numbers; for the record mine is currently 4 (me, Norman Paton, Mike Cornell, Pedro albeit via a genome paper), although if I get lucky with a paper under submission this will go to 2 (you'll have to wait to find out how...).

As he says, it's rewarding to observe how bioinformatics has moved on to become central to all biology; of course, it's also amazing how the web has become commonplace to the rest of our lives. At the time, it was image-poor, slow and clunky. Most of us hardly knew how to use bookmarks (if they'd been invented then, I don't remember), search engines were in their infancy, URL naming was inconsistent and changeable; it was really hard to navigate, to discover. It's perhaps not surprising that the website was such a success and remembered so fondly; the only question that remains is, how the hell did everybody find out about it in the first place?

His comment finishes with the statement that "And, if there is a final message, [it] is that with some good will, anyone can make a difference in Biology and elsewhere." What a cool bloke!

Anyway, in case my comment engine goes awry, I reproduce the quote here...

Where has Pedro gone? Well, I've been happily busy researching and teaching on my favorite subjects.

After a PhD in (Bio)Chemical Engineering at Iowa State University (ISU) in 1996, I did a Post-Doc in Grenoble and Marseille, France. In 1999 I got a faculty position in Biological Engineering at the Instituto Superior Tecnico, Lisbon, Portugal. From 2002 onwards, I moved to a new a faculty position at the University of Provence in Marseille, France where I presently teach Biocatalysis and Bioinformatics.

Since 1998, I've been developing and maintaining a database on Carbohydrate-Active Enzymes (CAZy,, that presently constitutes a reference resource in Glycobiology and a research tool for Glycogenomics.

The "Pedro's Biomolecular Research Tools" adventure lasted from late 1993 to early 1997. It was a great learning moment for me and I'm proud of leaving my little brick on the wall of Bioinformatics. Initially developed as the web complement to an internal software locker that I maintained, the list grew up in importance thanks to the positive response from the burgeoning community of web-aware Biologists and the many encouragements and suggestions I received from users from all over the world. It was a (hopefully) good index for those pioneering days where I intuitively tried to reveal the potential of the new discipline. Naturally, I used my on research subjects to test the different tools available at the time, and this had some impact on my thesis. However, the most rewarding and interesting was to observe how Bioinformatics moved on in a few years from an obscure and marginal discipline to become absolutely central to almost all aspects of Biology and its applications. As a community, Biologists created since then an impressive dynamic that makes other scientific communities envious. And, if there is a final message, is that with some good will, anyone can make a difference in Biology and elsewhere.


Back to a flying start

Yesterday was my first day back at work, after the Christmas break. It also turned out to be the teaching away day, where they callously blocked internet connections (aarrgh!). Today, I am on the train to Oxford for an Ontogenesis meeting. So. I've decided to read my email on the train.

1647 personal messages (not including mailing list) of these about, say, 1 in 10 were real the rest spam. Perhaps the most surprising, was an email from Barry Smith with subject "Be my partner". Me and Barry have been discussing for a while his flawed ideas about the building of ontologies; some of the emails got quite heating and the threads very long. I'd had no inkling that, during the course of these discussions, Barry had developed such feelings for me. Sadly, the email turned out to be asking for help transferring 6 million US into the country, which is perhaps less plausible.

We're now well past Durham and I'm almost at the end of the weeding out the spam. Reading begins soon.


Just finished reading my email. Just about to pull into Oxford. Not too bad all things considered.


Diamond Songs

Finally watched Blood Diamond this weekend. It was good actually, kind of an adventure flick but with an attempt to show some of the reality of the blood diamond trade. Of course, along side the brutal killing, child soldiers and arm chopping, Leonardo DiCaprio and Jennifer Connelly added some standard holywood magic to the whole affair; three stylists between then, made sure that hair was never out-of-place. The black African lead managed to achieve his apotheosis in the end by wearing a suit and talking to Americans (who could ask for more?). And, of course, there was a dramatic love interest to set it off. Still, it wasn't anywhere as bad as it could have been. It did help to raise child soldiers up the agenda, it did describe how the diamond market works (or worked as it's all different now, honest) and it was actually quite interesting. Critically important, there was no warbling in the background from Celine Dion which is guarenteed to improve any movie.

All in stark contrast to Carla's Song which I also saw; a simple, elegant and well-told story and some excellent performances. One of Ken Loach's more cheerful films with Robert Carlyle in his golden period, I greatly enjoyed it. If Ken Loach really wanted to change the world, he's spice his films up a bit, like Blood Diamond, to sell to the US market, get the message in under-the-wire. I'm glad he doesn't.



So, I've been using Lua for a couple of months now; I thought that I would learn it because it's been ages since I learned a new language, and it's got a reputation for being small, clean and fast.

On the whole I think it's lives up to it's reputation. It's a nice langauge, leaning more toward the functional than OO, at least in the way that I write it.

Syntactically, it's very simple and regular which is a good thing; there are a very places where I would have simplified it still further. For example, both of these are legal:

print( "hello" )
print "hello"

which is a nice syntactic short-cut, but then it only works with a single argument,

print( "hello", "goodbye" )
print "hello", "goodbye" -- ILLEGAL

Probably I would not have allowed the shortcut.

Lua has a pattern syntax for regexp-like searching, but in a desire to keep Lua small, it's a pretty weak; more over, it's not a standard syntax at all, and lacks familiarity. Of course, Lua makes it easy to link in a regexp library, but I think that they should have standard extensions — i.e. if you are going to link in a regexp library choose this one first. To some extent, this already happens — the Math.power function is not guarenteed to work as it forces the linking of the ansi C math library.

Almost all of Lua is based around tables — hash maps effectively — which also serve as arrays. This is okay and, of course, you can build anything you want from this; but, combined with the lack of types, I find myself asking questions like, is this a table of tables, an array of tables or a table of arrays? Too much knowledge is implicit. Table handling is also a bit limited; there's no support for taking slices of tables (when used as an array), nor functions like "contains" or "first index".

On the whole I think it fulfils it's purpose; it's great for small and simple code. The worry is that people will get carried away and start writing enormous applications in it, for which it is just not suited. Small languages have a habit of becoming big. As it is, though, it serves as a nice, relatively low-level language.


New Year in Italy

So, for the second year running, I've spent new year in Italy. This time, I've been in the North. A very different kettle of fish from the south and Tuscany. The drivers are much better, although I've still seen three road accidents, one of them quite serious, at least for the car; drive slow when there is ice seems the lesson.

I've been staying in Gavardo; this is a small town which is about 200m above Lake Garda. It sitting on a glacial moraine, in a classic U shaped valley, with magnificent mountains in the background. It's got upper-course river and a canal which seems to have been constructed mostly for the purpose of energy and irrigation rather than transport. There's still hydroelectric power coming from it, and a old mill building which would have had five wheels originally.

Lake Garda itself is beautiful, with the mountains coming right to the Lake. There are a large number of villages and towns around the edge; the ones on the lake are shopping and accommodation orientated.

One tradition I didn't know about, was the presipio. The Italians seem made for these; essentially these are nativity displays, but they put the hut with three figures that Worcester has to shame. Gavardo had at least three, complete miniature towns, with lighting effects moving through the day, sound, snow, rain and smoke (well steam I think) coming out of the chimneys. Most of them are static, but some of them are mechanised, with hundreds of moving figures. Perhaps to my surprise, I've also discovered that I am appear to be a few centrimetres taller than the average Italian; the presipio's are tunnels you walk through and I kept on scraping my head; just a scrape rather than a full headbutt, Japan-style.

I also went to the bath in Morano which is in the South Tyrol; it's a German-speaking part of Italy (or bilingual anyway). The terme there are magnificient; lots of pools, and a closed, adult-only sauna area, where I got to sit outside, in the buff at -2C, surrounded by snow-capped mountains, cooling down from sauna. Clearly, the Germany language isn't all that has remained here; I got told off three times for not obeying rules (sauna "au naturale", keep your feet on the towel and don't talk too loud. Eech.

Moreno was a day trip from Trento; I know some people from the University quite well, but I've never been there. It's a magnificient city. The architecture is constrained, but beautiful, but dwarfed by the mountains surrounding it.

It's been a good trip, but I'm looking forward to flying home tomorrow. Being surrounded by a foreign language can be tiring at any time; in Italy it's made slightly worse because Italians tend to talk loud (i.e. shout). So I'm suffering from a sensory overload, and there is a bit of hyperreality about everything.

Back to a school away day to start the year on Monday. Perhaps hyper-reality doesn't seem so bad after all.



It's been said alluded to before that I am, occasionally, an obsessive, with a tendency to think about totally unimportant rubbish and that I should get out more. Clearly, a post on video connectors is necessary here, for me to clear the air.

See, I just got myself a big new monitor at work; no doubt some people will impune that this is a method for making up in my lack of prowess in other areas; probably they are right. But it's left me wondering.

For years, monitors all had that strange 15 pin thing, always blue. Everything plugged into everything. Then, a short while back came out the DVI connectors; these are slight offwhite, with a novel combination of flat and round pins. My new monitor has an HMDI connector. But the other end of the cable is a DVI; my old monitor used DVI plugs, has no been downgraded to a second screen. Fortunately, it also had a VGA, which is lucky because the video card has one DVI and one VGA.

What's going on here? It's totally confusing. If I want to swap computers and monitors around, I have to sit and add up, do they have the same interface, do I have the right converter cables if they don't (or if I only have convertor cables, do they have different sockets).

It feels like the bad old days before some bright genius of usability invented USB; a flawed genius because they were stupid enough to make them rectangular, but a genius non the less.

It all goes back to what I was droning on about in the pub, on friday; it ended up like a comparison between different operating systems, cause I was a bit too drunk to make myself clear; I move between linux and windows freely, and given the choice, I decide on relatively trivial grounds; it makes no difference to me, really, because I can make them largely look the same anyway. And this is the point: what do people want from a computer these days? My answer is this: forget the features give me familiarity; stability not excitement. Just don't change a damn thing. And that includes the background wall paper.

Likewise, video plugs. We have three different sorts now. Stop it guys, just stop it.

You think this is bad, don't even begin to get me started on low voltage power supplies...


Home from Workshop

Well, it was a good meeting. I enjoyed listening to the talks, although I frequently found myself a little out of my depth; perhaps both a sign of how much biology I have forgotten and how much maths I never knew. Also, I think that the conference was not ideally weighted. Some multi-track, shorter talks, I think. It felt rather like the early eScience All Hands meetings.

On the way, down almost all the Newcastle people travelled together; for some reason, on the way back, we all scattered and went different routes. I thought I was on my own, going through Sheffield, but bumped into a fellow Newcastle academic on the platform, in the shape of Tom Kirkwood: Professor of Gerontology, former Reith Lecturer, and all rather clever chap. What brilliant and incisive obervation on the state of systems biology did I make? What stunning analysis of the impact of the RAE results did I posit? "Hello," I said, "did you get the train to Sheffield too?"

Still, it isn't all bad; I did manage to proof conclusively that it is possible to survive for three days eating only two of the major food groups: fat and carbohydrates.


BBSRC Grant Holders Workshop

So far, the BBSRC Grant Holders Workshop has been fascinating. Dennis Noble's talk last night, including an entertaining slagging of the Gene Ontology; entertaining but as wrong as you can be when you confuse a gene name and a function. Nice to hear a new variation of the Syndney Brenner "but an ontology doesn't allow you to understand all of biology" argument.

I also learnt that a) without convection it would take 10,000 years to make a cup of tea (unless you invent a spoon) and b) there are, on average 8 sausages in a tin of sausage and beans and, further, that the distribution of sausage number is low enough that the machine that puts them in the tin must be counting.

I also learnt that some people have too much time on their hands; that I am blogging about this means I have to include myself in this category.


Farewell, John Rebus

I finished Exit Music this morning. I've been reading Ian Rankin's novels for nearly a decade now starting, perhaps ironically, just after leaving Edinburgh for London. I still think Black and Blue is the best, although Tooth and Nail is my favourite. I heard Ian Rankin say once that as he'd just moved to London and was feeling miserable, he's inflict the same onto Rebus. As I was hating London also, I emphasised greatly with the book. Also, it's got a keystone cops, comedy car chase at the end. Both author and detective moved back to Edinburgh fairly shortly afterwards. I never did, although I did leave London.

The last book is good and a suitable ending. Like many of his more recent books, there is a random, unresolved element to the plot. But it's exciting, page-turning and a suitable finish for the series.

Having said that, it's probably a good thing that it's coming to an end. The books got lots of moody, black and white shots of Ian Rankin, with readers notes and meaningful questions about the use of metaphor for reading groups. Doesn't detract from the novel, but is, really, deeply pretentious.


Get Well Soon

I had cause to go doctors recently; I thought, I'd try the new drop-in centre that they have opened in town. It was fine, for the record, although I can't really see the difference between this and a normal doctors. Well, with the exception that they don't have the appointments fiddle (we guarentee to give you an appointment with 48 hours, but not giving you an appointment which is further away).

Next day, I get a call from my own doctors — were they phoning up to send me a get-well soon. No, of course not, they were phoning up to sign me off; the receptionist seemed quite irritated that I had been to the drop-in place, and had great pleasure in telling me to seek a new doctor.

The problem was, of course, that I have moved, so I am "now no longer in their area". Yeah, but I only go to the doctors once every couple of years, on average, and I move on average about that often. So, theoretically, I would have to register with a new doctor about as often as I want to see one; hardly surprising, then, that I can't be assed to register at all.


Jolie Holland

Been looking forward to Jolie Holland for a while; I think her records are superb, from the Be Good Tanyas onward. Her strange, wierd vocals seem to work; Mexican Blue is stunning song, which leaves me lost everytime I hear it.

I guess this is a lot to live up to. Last nights gig missed by a mile. The support, who's name I forgot, was poor; nice voice, but the songs were crap, and the performance shambolic. This was replicated by the main act; she treated the audience like they were the wall-paper at her own private practice session. The band spent lots of time talking to each other; they had to tell poor jokes while she tuned up, which took ages. And she needed it; the first three songs were played with an out-of-tune guitar, that was mixed up loud enough that you couldn't hear her voice anyway.

God knows, I'm not a performance fascist; I like things relaxed, I don't mind raw and I'm not a technical freak. But a live performance is just that — a performance; if you can't be bothered, then you shouldn't be there.



At the SWAT4LS meeting in Edinburgh. After the melee of teaching over the last two months, it's a real delight to be back in a research environment, to have some real quality time writing emails, while someone is talking in the background.

So far, it's been pretty good. I'm surprised by the size (75+ delegates) and the large number of papers submitted (40ish). They seem to have really hit the time right. The talks so far have been interesting; lots of integration, lots of querying, and far more architecture diagrams than I want to look at in one day.


John Martyn

John Martyn has been around for donkey's years. Sometime, in the 80's he decided that enunciation was for wimps, and he started to sing like a wookie. More recently, he's lost a leg, put on enough weight that resembles Jabba the Hutt (two star wars, references in one review; hmmm). He must be passed it now.

John Martyn started off as a folkie, more or less invented trip hop along the way; his music is mesmeric and beguiling. In his prime, he could take the stage on his own, with his Les Paul and fill the entire room, entrancing the audience. I think he was the second musician (not including the pub blues bands that were the stable of my youth) that I ever saw live. I've seen him from the North to the South of the country; Solid Air graces my mp3 player at great regularity; in many ways, he has been a critical part of the music that has changed me from the time we got our first record player, to the washed out, muso, gig junkie that I am now. He is passed his best now, but he's made up for his own lack of mobility with a band, to fill the sound that he used to. This tour is the Grace and Danger tour; the music was sad and heart-breaking at points. Solid Air itself has been lent new immediacy, for me, with the loss of a good friend to suicide earlier in the year.

This was one of the most moving gigs that I've been too for years; I was left silent till the day after (unusual for me). One of the best gigs of the year.


Music Madness: Stephen Stills and Erik Mongrain

It's all gone a bit mad since October. I've been to so many gigs that, combined with the start of term, I haven't really had time to write them all up.

Stephen Stills was my first gig at the City Hall; cool venue inside, dramatic, good looking, comfy seats. The sound is pretty poor though. I was sitting a way back, but on the balcony and right at the front of it so the view was excellent. Being at the gig made me feel young; it's rare that I am in the lower quartile of the age range these days. There was an element of homage about the whole thing; there were two old hippies in the front row who clearly got stoned to CSN (or maybe Buffalo Springfield) when they were young and were going to cheer regardless. But, it was a good gig. His voice is a bit wavery with age — he murdered "Change Partners" — but his guitar playing was generally wonderful; I think I preferred the acoustic half to the electric, but both were strong. It was all a bit dad rock, but it was still good.

Erik Mongrain I've not seen or heard before, but he's made a splash on YouTube. This was in the same series as the Bob Brozman gig that I went to earlier in the year; their advertising is still chaotic. It was 10 quid to get in, but half price because I am on the mailing list (which I don't think I am, all although I tried to be). The venue was in North Shields. The box office phone was redirected to a random office somewhere, and never answered.

Gig was great through. Erik's clearly a technical genius, playing intricate, complex music uses both hands interchangably to make music — he strums with his left hand, fingers with his right. All very guitar hero stuff. He's also quite shy, and retiring. He often described what his songs were about, but the descriptions were usually incomprehensible; regardless, there was a wonderful meditative feel to the evening. You could listen and relax and let the music wash over you.

I hope the series continues, because they've got some great players. But, if they advertise so badly and carry on making it hard to get tickets, it's not going to. Enjoy it while it lasts.


The impact of Organophosphates

This paper surely has to win the prize for the most entertaining title of the year.



In the basic biological sciences, statistical considerations are secondary or nonexistent, results entirely unpredicted by hypotheses are celebrated, and there are few formal rules for reproducibility


Now, that is what I call a real quote.


Where has Pedro gone?

In the dim and distant past, Pedro's list was this amazing resource for biologists. Speak to anyone of my age, and they will remember this list; in the early days of the web it was the best place to go, to find out where to find your bioinformatics tools.

Pedro's list hasn't been updated since 1995. There are still copies of it around which google will find for you if you want. It turns out that Pedro was, in fact, Pedro Maldonado Coutinho who was a graduate student at the time. A little more poking uncovers his thesis from 1996; this explains why he stopped maintaining the list. A little more poking reveals very little. He worked in France for a while but then disappeared from the web record. A later google hit suggests he might not have left biology altogether — but it's hard to tell for sure.

Pedro, early web pioneer, I salute you!


Out and About

This weekend was also lovely; this time I cycled to the coast, then up to Beddlington, across toward Morpeth. By the time I got to the Morpeth road I was exhausted. I guess 12 miles up hill, against a wind will do this to you. So I cut out Morpeth and just came home.

42 miles in total. Too far, I fear. A bit disappointing as it should have be fine; less than last week and with a lot of road involved. Went at about the same speed too. I have some way to go before I can get to the 100 it appears.


Blogs and Bazaar

Well, the new version of the software for this website is nearly done. I'm onto muse generation now, having got the scary make file and perl file generator done.

Of course, you could ask the question why not switch to wordpress or blogger or the like? Well, at the end of the day, I have to have an offline tool. Also, I like to have all my source files locally. All my electronic work is based around a single directory, and everything is in there. I guess that I am far from being a convert to the cloud.

It's probably going to take a few weeks yet, though. There should be only a few visible changes; first I am moving toward tags rather than categoies. I will be adding more than the current four. This means the individual RSS feeds — there will be only one. I doubt that anyone will mind this, but should if not.

My experiences with bazaar continue. I've used it to version my new blog software and, also, all my course notes from this years teaching. I've had one inexplicable crash (it core dumped everytime I tried to init one directory). In general, though it's really nice. It feels like going back to RCS in some ways. You don't have the SVN and CVS nightmare of importing a new project which tends to involve moving existing files out of place, then checking them out back into place.

I haven't actually tried any of the distributed facilities yet; it's all just me for which SVN was always overkill anyway. It's nice to know that I will have the option when I get to it.



I decided that I was going to try and cycle to Hexham to do. It was a perfect day for it, but then I haven't been out for a long bike ride for a while. I've been a lot of the way before, but forgot my map; not normally a problem on the road, cause you can follow the signs.

This time, it was more of a problem. I got as far as Corbridge and then decided to come back; when I got home I found I was only 3, maybe 4, miles short of Hexham; if I'd had a map, I'd probably have known. Flip side is, I was pretty popped when I got back; the extra 9 miles might not have been a good idea. As it was, I managed to do 45 miles, which was not too bad.


It continues...

My adversary even responded to my email which ended with "I think it's time to stop this". I replied with an email saying "But I am going to get the last word". He replied to this as well.

He's turning out to be quite a nice guy; he's accused me of "displaying an incredible ignorance of the FLOSS community" — my reply was that I just didn't know what the acronym was and that this was probably a good thing.

Although, I'm really quite warming to the guy, there is a problem here. I like to witness the development of a community, but in many cases this seems to result in introversion and worse still exclusion. Regularly developing a pile of acronyms, like the tendency to generate new jargon in science, just services to exclude people. Having switched between quite a few different disciplines, I've been on the wrong end of this tendency to find a clear reason why someone else doesn't belong. "Ah, but our community isn't like that", "We're not the same as them though, so how can their solutions be of value?", "But you don't understand how we do things". It's a shame and it saddens me that people who are essentially good should still fall prey to it.


Fall out from Neuroinformatics

Well, there were a large number of specific outcomes from Neuroinformatics 2008, most of which I won't bore you with. The best idea, though, came out as piece of humour. I was ranting (yes, I know, it's hard to believe) about public understanding of science. I'm a bit fan of this because I think that as scientists we should be able to write about what we do clearly and at a level suitable for an intelligent but uninformed individual. Of course, I believe this because in Neuroinformatics, this covers me; I don't know much about brains, just computers and biology.

The suggestion was that, to every scientific paper we publish, scientists would be forced to add an explanatory paragraph; now, as I say, this was meant as a joke, but I think it's a great idea. It is the beginning of term, so it's going to take a while, but I intend to do exactly this; I shall add explanations to my publications page for each of my papers. I'm slightly worried about this, of course; it's a well-known secret but, like many scientists, I don't actually know what all of my papers are about; some of them were written by other people, some of them were written by me so long ago that I was "other people". So, I might even learn something in the process.

I shall announce releases here; the world will, no doubt, hold it's breath till it turns up.


Cygwin Bug Reporting

I managed to find a solution to the problems with Bazaar; the problem is that vc-bzr.el launches "bzr" which is a python script; the cygwin version uses a magic shebang line which doesn't work on windows outside of cygwin. So, firstly, I fixed the problem in vc-bzr.el by making it launch the python executable directly and then pass "bzr" as an argument; I sent this into the Emacs Bug List. I got a reasonable reply from Stefan Monnier suggesting a wrapper script; I kind of agree that it's a nicer solution (it works with DVC too!), although it still leaves users in the situation of vc-bzr.el not working out of the box.

So I sent a report into the cygwin mailing and got replied with a blank no from the wonderful Christopher Faylor; just use cygwin or it's "do whatever you like". Meanwhile, off-list, I've been soundly castigated by another cygwin mailing list subscriber who has advised me "PCYMTNQREAIYR" and really doesn't like my quotation style. I never understood speaking with acronyms since I first met it in Perl land; but, hey, TMTOWTDI.

Some wonderful sections of the email conversation include:

  him> you can't be bothered to take 15 seconds to look something up, why
  him> should I be bothered to talk to you?

I don't know. And yet you are.

Astonishingly, he replied to this. It's been an entertaining conversation, but I think it's time for it to finish; I am hoping that this will work.

  him> I also care when you blatantly disregard the accepted practice of a
  him> community, and refuse to listen to members thereof when they try to
  him> tell you you're behaving in a way that is, by their standards,
  him> inconsiderate.

So bug reporting is inconsiderate? For the record, by the standards imposed by
my community, preaching at people is considered rude. I saddened that you
blatantly disregard these standards. But, hey, I'll get over it.

  him> A simple "I agree to abide by the list etiquette when posting to the
  him> list" would have ended this conversation long ago.

Yes, but then this conversation has been an entertaining diversion from my
otherwise dull and pointless existence which I would have been sad to miss.

I don't think I've ever received such a response for an attempt to publish a bug report. I guess some people need to just get out more; in this case, I mean me, but it's just about the start of term and that's not likely to happen.


Flats again

Well, things have improved somewhat. We have notice from the bank that the hearing will now no longer go ahead, which suggests that the landlord has paid. Also, British Gas came and fixed our heating; it took a long time to work out, but this consisted of turning a valve that the first plumber had switched off, back on again.

It's all pretty tiresome.



I've never been here before. but I like it. The Scandinavian countries all seem lovely. They are understated, quiet and have an effortless beauty about them. It's a wonderful place; the sort of place that I would love to spend some time in, even if all the road signs are incomprehensible. If I could afford to spend more time here, then I probably would.

Now it's late, so time to sleep.


Neuroinformatics 2008 — Day Two

Today, we have neuroinformatics meets bioinformatics. I've been looking forward to this; unfortunately, I'm feeling a bit washed out having slept badly. I went to be at 10ish (I was tired!) and went to sleep at 2ish. The room was too hot and, by bad design, I left my melatonin at home so I lack even chemical solutions.

We've started off with a talk by Ed Lein from the Allen Brain Atlas. Lots and lots of gene expression analysis!



I've started to give bazaar a go in anger; my hope was that I could get the offline advantages of RCS, with a newer system (renaming and such like) as well as something that works for collaboration.

The emacs support is a bit primitive yet. There is a vc-bzr.el, though, so I tried this but it didn't work. This turned out to be because it doesn't work with cygwin out of the box. I've tried the windows version and it all seems to behave nicely. But it doesn't understand symlinks which is a major pain — I need those symlinks!

Life can be hard at times.


Neuroinformatics 2008 — Day One

So far, we've had two talks, one from David Essen, one from Mary Kennedy. A nice bit of organisation because they have jumped scales — the first was mostly about brain gross anatomy and the second about molecular modelling.

A bit like it's forerunner — databasing the brain — there is not that much informatics here. The keynotes have been very much about the neuroscience; this makes it both novel and interesting for me, although fairly heavy going at times.

It confirms my feeling that neurosinformatics is much less mature than bioinformatics; it's not really a separate discipline yet. Not that this is a bad thing; I've been at bioinformatics conferences where the "bio" seems barely relevant. If I am honest about it, I think more about computers these days and sometimes forget the point — understanding life — although I guess this is inevitable working in a computer science department. Less mature is another phrase for new, young and fresh. It feels good to be in this environment.



Several months ago, I moved house. I should say now, that main reason for doing this was to move in with the other half; I only mention this because she was irritated that she got so few mentions when I was talking about our holiday. My explanation was this blog is called "An exercise in irrelevance" because it has nothing important in it and that she has her own blog so why should she want to appear on mine. Impeccable logic I thought; she didn't.

Anyway, coming back from the social melodrama, a few months ago, we moved house. It's quite a nice place; it's unfurnished so has required a lot of work buying furniture, screwing it to together and standing it upright (having, of course, carefully hoovered underneath first). Although it's left me tired and drained, I've enjoyed it. The flat, however, it turning out to be a bit of a disaster.

The letting agents, Countrywide Residential, have been fairly poor from the start. Obviously, this is all my misunderstanding, and is not what happened at all, but they appeared to phone me up the day before the lease at 4pm, say we were required to have contents insurance and then offer to sell us the same for 3 time the market average. My mistake, but it appeared to be a filibuster. Obviously, this is not what they did say, because the lease does not require insurance; probably, they were just trying to be kind and help us with some organising. No doubt, their deal was different from the ones we found on the internet and were no way comparable, hence the price.

We've now had the plumbers out three times to the heating system; once because the timer has broken, once because it was leaking and now, it's no longer leaking but it ain't working either. So, no hot water. Not too much of a disaster for me as I am going to Stockholm for a conference, but a pain for my other half (two mentions in one post!).

Still, this seems to be getting sorted now. But we got home last night to find that the Royal Bank of Scotland (my bank incidentally) is taking the landlord to court for repossession. For foreign readers of this blog of whom there are none, in most sane countries tenants have pretty strong rights; if you pay the rent, you stay in the property. In the UK, we have very few rights; you can get kicked out for little reason. One of the few rights we do have is an initial 6 month rental period; in that time, it's hard to get rid of a tenant. Unless the landlord doesn't pay his mortgage and gets repossessed. Under these circumstances, you are out. So, potentially in a months time, having not quite moved in yet, we'll be putting everything into boxes and moving again; in the middle of teaching term also.

As a society, I think that we have to learn that rising house prices does not constitute a boom and that falling house prices a recession. Both of them are a disaster. Steady, reasonably priced, affordable houses are the only way forward. It's about time that we grew up from our free market childishness and realised that a house is not an investment, it's something to live in.

For us, the worst case outcome is not a disaster; it's an inconvienience, a cost and a lot of hassle, so I'm not depressed, just irritated. I know for many others, the situation is much, much worse.


Neuroinformatics 2008

Ah, off to a conference again. Depressingly on saturday, so the airport is heaving. I'm going to Neuroscience 2008 which is a new one to me, in Stockholm which is also new. I'm taking a poster which seems distressingly old. Been a long time since I've done this. It's already been a struggle — some of my colleagues didn't like it; I think because neuroscientists tend toward lots of text, while I do a light-weight, advert-style, if-you-want-more-details-read-the-paper form of poster. And I hate travelling with a poster; it's hard to replace your belt while carrying a bag and an A0 poster tube. My subconscious tried to leave it at a Starbucks in Schipol, but my better judgement forced me to go back for it.

I'm not in the best of moods: my toe, which I appear to have broken is nothing but a a dull ache and I was frozen on the flight having got a bath between the terminal at Newcastle and the plane. Still the conference should be fun.


Keelmans Way

I managed to get our on my bike at the weekend; I travelled up the north side of the Tyne. I've done this before, but went further, through Wylam and out the other end; it's a really nice ride, although not that fast as the surfaces are a little rough. In the end, I decided to come back on the south bank, as I've not done this before. Took a bit of to-ing and fro-ing, but I mostly came down Keelmans Way. The Gateshead side of the Tyne is more industrial than the North, and Keelmans Way reflects this; instead of fields, pubs and villages, you cycle over steel bridges, peers and through industrial estates. It's still quiet, though, and great fun. I have to admit, though, as I came into Gateshead, that I was gob-smacked when I cycled through a gap in a hedgerow and found myself on the ring road of the metrocentre. I had no idea it was so close to the river, and that I was so close to it.

Only managed 30 miles, but this was mostly because I had other things to do. I want to try and up this. If I can keep going over winter, with any luck, I should be able to do the 100 mile in next years cyclone.


Water flow

Been having problems with my water tank. At first, it appeared to be the tank itself; I ended up with a frying pan underneath to catch the flow. Eventually, I realised that it's the pressure meter at the top of the tank which is the problem; the water was coming down the side, and dripping from the bottom. It's only dripping which is why it took me so long to work out where it was ultimately coming from. But it's leaking maybe half a litre an hour, which is a lot of water over time. However, because the tank is close to the ground, I could only use a shallow frying pan to catch the water. My solution to the problem is a Heath Robinson master-piece.

I've wrapped a piece of cloth under the leak, which has got soaked. This then directs the moisture away from the tank, where it can drip freely and be caught in a large container. The dripping was going to drive me mad, however, and also as the cloth got wet, it changed it's shape; so I added a funnel and pipe. The last essential ingredients were some cling-film around the cloth to stop drips from anywhere else, and vaseline on the water tank to re-direct the last few recalcitrant flows.

Full details available.



I've been to Gerswhins, which is on (or under) Dean Street before, but for a quick pre-gig meal. This time was a more leisured affair. The place is underground, in a wine cellar. It's dimly light, from 100s of fibre optic strands from the ceiling. It's a jazz resturant apparently. So, later in the evening, they had caberet; a guy in a dinner jacket, crooning to a recording backing track. He was actually pretty good, very professional and a competent singer; half-way through a Sinatra melody, an older couple, very elegantly dressed—man in blazer and tie, woman in skirt and formal top—started wheeling around the dance floor (that is the small gap between the tables). The woman looked happy and entertained, the man dignified and serene, although I noticed a momentary look of relief as he got to sit down again.

I could help thinking that the dimness was partly to cover up the flaws; there was a ice bucket hidden partly next and partly under my seat, catching drips from the ceiling; or at least the ones which didn't fall on me. The toilets were dark, but with spotlight urinals which were stainless steel; the parabolic bowls shined the light back bright enough to burn your retinas; while engaged, however, my head blocked the light and, already half-blinded, meant I had to aim using echo location. And one of the taps was not screwed in properly, rotating Exorcist style rather than producing water.

A strange night; Gershwins is a bit tacky, but gets away with it for some reason; it was both elegant and naff simultaneously, which should be impossible.

Oh, yeah, and the food. I had a pepper and courgette soup followed by a mushroom curry; they were both excellent, even if the curry was a bit pokey. I had a pepper soup a couple of weeks ago (on the Grand Canyon of all places) which was lovely, so perhaps I should try this.



So, first time I've been in the US for a long period on holiday rather than working. It's still a country that I don't understand, a place of contrast and contradiction. In it's care for the National Parks, you can see the place at it's very best. It's caring, educational, passionate. At the same time, staring across the Grand Canyon or from Joshua Tree, and understanding that the haze you can see is pollution from the roads of Los Angeles is a depressing experience. It's a pity that more Americans don't do as I have done, and visit the national parks to see the damage that they are doing; there's no excuse; it's so easy by car.

I've enjoyed the US away from the main urban areas far more than the time in the cities; touring through Arizona and Utah has been a great experience. Perhaps the most unexpectedly educational experience, was listening to Rush Limbaugh and his equivalents on talk radio. Clever and consistent, it's easy to see how this trickling propaganda sinks in. Being able to switch your opponent off, makes it easy to win the argument.

For the leader of the free world, I find the US strange constrained; there are signs up everywhere telling you what you must or must not do, all backed with obscure references to ordinances. The exception to this, of course, is parking which you can do most places. Even the rich districts of SF have 2 hour parking on most streets. At the same time, basic consumer protection seems missing — the price you see is never the price you pay, even if it's just tax. Having said that, everybody is willing to do things for you, if you ask. You can get food as you want, variations are almost always possible, and if you are argue rules can be changed; in the end, we didn't pay the one way charge the San Diego branch of Dollar was trying to screw us for.

The low point of the holiday has to have been the MGM in Las Vegas; two lions in a small glass cage in a Casino is a disgraceful exhibition that degrades all those who see it. The highpoint was Betatakin floating in the distance. And the most pervasive memory, I steal — all the roads going, all the people dreaming in the immensity of it all.


Hill and Bay

Yosemite is one of the oldest and perhaps the most complete of the National Parks from an enjoyment point of view anyway. To get into it, we went over a 9900 foot mountain pass, crawled down to the valley floor, with temperature raising as we went. I saw El Capitan (or a big rock for those not in the know) and the US's tallest waterfall (impressive, but almost dry at this time of year).

The whole place was wonderful, but it's got such heavy traffic through it and it's less well done than Bryce or Zion in terms of information. Ultimately, I think that the problem was ours; vast amounts of Yosemite are only accessible on foot; clearly the short time we had, is not the best way to see it.

San Francisco was great, however. All of a bit of a cliche I fear — the hilly streets, the crookedest road which we drove down by mistake, the cable cars and so on. I've now sailed under the Golden Gate bridge on a catermaran, been on a cheesy tour in a bus dressed up like a cable car. It's a vibrant city, relaxed and comformtable. The climate is nice, never hot, never cold; although, ironically, having been in the desert for 2 weeks, I burnt my head — it's cool, but the sun, when it's out, is as bright as anywhere else in California.


Desert and Mountain

It may seem that we are ticking off national parks in a mad rush, but it's not really the case; this trip hasn't allowed an in-depth study of the Parks it's true, but I think I've managed to come away with an understanding of the essential nature of each, as well as a deep appreciation of local sandstones.

After Bryce, the plan was to move to Las Vegas, but Zion stands more or less in the way and we got sidetracked; which was good as Zion is one of the most beautiful parks I've seen, with the most amazing variety of micro-climates. The main difference is that it has water; so while it's still desert, it is rich with plant and animal life. As you move upward, it gets wetter and cooler and the plants change accordingly. Perhaps the most extreme example is Weeping Rock; this is a enormous rock face which sits on the boundary of two layers of horizontal rock, the lower layer being impermeable; so water that fell as rain 1200 years weeps out onto the desert floor causing a small, local swamp area. In a 200m walk, the plants change completely.

Zion has also had a novel idea, which the rest of the National Parks should learn from: they have banned cars from the main road. We toured the valley in a propane-powered shuttle bus. The view was better as a result and the place more peaceful. Bryce and the Grand Canyon should follow. Arches and the Petrified forest might be a different thing; a 5 minute wait for a bus in Zion is nothing, but in the full desert heat, a car also becomes a portable air-con unit.

It took 4 hours to see Zion, so we stayed in Hurricane rather than Vegas as was the plan. A classic American town which I did not see much off.

Next stop was Las Vegas itself. For specifics, read a guide book; Las Vegas, at least this part, is surface thin. It's visually stunning, provides a sensory overload, but there is nothing to it, other than the things you can see. More over, even the shows seem to be largely a copy; the number of people who were appearing as some one else, from stars of Country and Western, to men dressed as Joan Rivers or Brittany Spears. The whole place was plastic, packaged and artificial, even down to the food; the closest we could get to real food was bottled orange juice and a prepared fruit salad.

From Vegas, we travelled through Death Valley which was 48C at the lowest point that we got to (190 feet short of sea-level). Stark and magnificient, dangerous and inhospitable, it was everything that I could have expected.

Out of Death Valley, we have passed the shadow of the High Sierra Nevada, including the highest mountain in the main body of the US. In the distance, I saw the smoke from a major fire in Yosemite; we've come to rest in a place near Crawley Lake which doesn't seem to have a name of it's own. The temperature has gone in a few hours from 48C to around 10C. Outside, I've saw in 5 minutes the milky way, three meteorites and the sky lit up with a distant lightening strike.


Arches and Needles

Been to four more places since Grand Canyon. The first, Monument Valley is actually part of the Navajo nation. It's got a famous skyline, but it's not been that well developed and not that great as far as I can tell.

The big surprise of the trip was the Navajo national monument — managed by the federal government, but named after the Navajo. It's not that big, but you can walk down short trail which overlooks Betatakin. This is Pueblo settlement, maybe 800 years old. It's hidden in a large cave, shetlered from the elements. I only saw it from a kilometre away, but it was a wonderful experience.

Next, came a brief stop in Moab; they have a small museum there, with most of the exhibits appearing to come from a few families whose descendents were or are compulsive collectors; one of the items was a trunk from a chap who came from "Trimely, Worcester". I suspect this was Grimley in reality, but it was strange to come around the world to find a peace of home.

The Arches National Park has lots of, well, arches. Truely amazing place, you can stand under fins of rock weighing millions of tons. Hot as hell, though. It must have cleared 39C.

Finally, today was Bryce. As far as I can tell, it's made of very similar stone to Arches, but it's higher up (about 3000m!) and wetter. It's been formed by freeze-fracture rather than gentle (and very rare) water. As a result, the rock formations are spikier, rougher and stunning. They have formed a wonderful canyon; in many ways this is more impressive than the Grand Canyon as you can easily walk into it, feel the sandstone and, most of all, look up.


An old forest and a big hole

In an ongoing attempt to tick off as many national parks as possible, we've now been to the Petrified Forest. It's basically a desert with a lot of stone logs in it. This doesn't quite cover it though; the fossilized remains are so dense at points that you would believe that they have been placed there, but it's actually natural. Although it was hot (about 36C I think), I seem to have acclimatised now; keeping the air con off in the car helps. This gives you the freedom to walk around at peace, except for the need to consume water and factor 50 sunblock in roughly equal quantities. Ironically, the two best sights, however, were not the fossils: first, newspaper rock which is covered in 1000 year old petroglyphs — there are literally 100's of them; and, second, the sunset. The sky was deep red, with a cloud just above the horizon, light up with a bright halo.

Now, I am in the lobby of the El Tovar Hotel; 20 seconds walk outside the door is the south rim of the Grand Canyon. I don't know what to say about this that is not obvious; it's really big, very colourful and awe inspiring. Walking around it for a day will stay with me for quite a while.

Without wishing to be a party-pooper, I think that Waimea Canyon on Kauai is actually better; it's 1/20th the size but it's also very wet, teeming with life.


I have climbed highest mountains....

Well, okay, so actually we drove. From San Diego, we drove straight to Indio, which is just south of the Joshua Tree National Park. Got there to late to do anything; to be honest, the area (Palm Springs) looks like there is little to do except bask in luxury of expensive hotels. The next day, we drove through the Indio mountains; this is edge of the desert proper and was, in a nutshell hot (38C) and dry.

The Joshua Tree park was $15 to get in with a car; money well spent. It's full of Joshua Trees as you might guess, but also amazing rocks, cactus of all sorts, animals, a hidden valley (which really is hidden, I got quite nervous when the exit was not where I thought, but another 100m on). The sunset was wonderful.

Today, we drove across the Mohave desert, or at least the outskirts of it. The fuel gauge just went shooting down, as the air con fought against the desert heat. We skirted London Bridge (for this is where it ended up) and then caught Route 66 (which isn't called 66 anymore). Oatman clearly lives entirely on tourism; it's complete with Tavern, jail with gallows and, bizarrely, semi-wild ex-pit ponies. It was actually less tacky than you might think, and the journey there was fabulous.

After that, we headed to Flagstaff which is where I am now, in a motel. It's pleasant and cool, being at a little over 2000m in elevation. The motel is on Route 66 again. It's also next to the Himalaya Grill; no idea why they called it Grill; nor Himalaya as it's not basically curry, although with anise and a few other unusual spices. Well, suffice it to say, I am now very stuffed and rather happy.


Cars and Cactus

So, two days in San Diego; it was a busy place. Comic Con was on; I've never seen so many Jedi in one place, although the Boba Fett's made a pretty good showing.

Most of the stuff that I saw in San Diego, I've been to before; the exceptions was Balboa Park — very nice indeed, lots of museums, including a botanics and a cactus gardens — and Coronado — chilled out, lovely and, no doubt, very expensive.

Also spent 3 hours in car hire places. A throughly irritating and unpleasant experience. I was taking back one car and taking out another. The first car had some bumper marks on the rear; apparently this required urgent buffing to return a hire car with 80,000 miles to full service and this would cost $75. Much arguing with the idiot cliche of a hire man ("is this how you do business?"). In the end, paper and water cleaned it up. I guess that I should not have been surprised by a car hire place called "A1 Budget Hire", but it was tiresome.

The second place, this time Dollar Car Hire, decided that we hadn't paid them enough and they should charge $200 extra, for a single way journey. This is after an 2 hour wait in the queue; this one, we are going have to take up with the credit card company.

Ah, well, onwards and upwards; we have moved to Indio which is inland and in the desert. No idea what it's like as it was dark when we arrived except that it's really hot; yeah, well, I guess it's a desert.


Due South

Yep, so Portland is definately not so bad. We ended up in the Irish pub last night, which was fine up to the point they started the pixie music. Then we moved to a second pub, which was book-lined and made you go to the bar to get drinks. Much nicer.

I hit the sack just after 11 — I was really tired, and unable to count how many beers with the combination of pitchers and variable glass size.

Now in Portland airport, heading south to the hydrocarbon assault of San Diego.


Walking by the River

Okay, so it's possible that I was a bit rude about Portland yesterday. I walked to the meeting today, down the river side past the multiple bridges. It was overcast, warm but not hot. I could have got a bus or streetcar, though; Portland has a good light-rail transit system, but multiple forms of trains, overhead cable cars. There's also good support for bikes as well, with a few bikes going past every few minutes. Maybe, I was just being a bit miserable yesterday.



At the interoperability workshop. It's small but focused. But there's no network! I don't know what to do? I might end up even listening to the talks now.


Portland, Oregon

Flying into Portland, it looks a really beautiful place. It's got a hilly, dynamic, green and water-rich landscape. The city itself, after this, is a bit of a let down to be honest. We're in the Benson Hotel — a local landmark the programme booklet tells me. It's at the edge of the downtown district which is small, yet tall. Small is actually good, as it's not far to get to one of the quieter backstreets where there is plenty of simple, cheap food. Heading North, the areas get slightly seedier (bar, then camping shop, then grocer, the full nude review theatre). After the vibrancy, relaxation and excitement of Toronto, it seems bucolic to say the least.

The Benson Hotel is nice, but somewhat tatty. They got all the frills — doormen outside, chandeliers, idiot guest at the front desk shouting out how badly he's been treated. The guest room, however, shows that while the attention to detail is there, they have forgotten the basics. The glass in the window has integrated The window frames are dirty and are single glassed sash windows, making the room cold; the heating (which you need as a result) has only a "hotter, colder" thermostat so it takes ages to get it right. The furnishings are all grand but have clearly seen their better days.

I think that I have finally understood the difference between US and European cities. In Europe, evolution and economics has given us strangely organised functional parts of town, with roads randomly and chaotically scattered throughout. The US cities have incredible organised roads with the functions scattered randomly; facely buildings, next a brightly lit shop, next to a bar and then a parking lot ($7 all day — land is not expensive here). I guess Americans get as confused by our winding roads as we do by their building chaos.

Maybe I am being a bit negative here; perhaps it's because I am being all sad and pathetic and not knowing anyone.


Back in the USSA

What a pleasure it is to be back in America. ISMB and Toronto were good, but now I've moved onto higher things and am in Minniapolis for a flight change. I entered the US in Toronto (er...) having cleared immigration there; end up in the secondary examination room (where's the vaseline?) having after first miserable enemy of humanity for an customs officer who didn't want to point out that "index finger" meant the first finger. Well, it was early.

I should mention that the two customs people in the backroom, though, were polite, patient and efficient.

On the plane, I had a moment of panic when the announced the destination as "Twinchitty", somewhere I did not want to be. Turns out Minneapolis is known as "the twin cities".

Stopped in the airport for some noodles and tofu. They were alright but the caramel in the soy fused with the addititives to leave a nasty aftertaste. So I went in search of some fruit; the cloest I could get is some banana cake and a small (read vast) expresso.

America, America, Land of the Free, tra, le da.


Skype Spam

Just got my first piece of skype spam...pretty novel.

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Upstairs, Downstairs

Got up yesterday morning (duh, duh, der, duh) to go the conference. On the way down in the lift, realised I'd forgotten my geek badge. So, went back up to my room. Realised, I'd locked myself out. So went back down to reception. Then back up to get my geek badge, then back out. 55 floors of movement. Hmmm.

I'm enjoying ISMB this year. Been flitting between SIGs and don't have to worry about bio-ontologies till tomorrow. Text has been quite fun. BOSC as often has some interesting subjects but with a big variation in the quality of the talks about these subjects. Biopathways had some nice stuff also, but the talks are a bit long and the program keeps going off time. Lucky that Mark Wilkinson's biomoby talk was early at BOSC, as I could pop out of pathways without missing two talks; glad I didn't miss that; exciting, energentic and with very funky slides, as always.


Long time, No Write

Regular readers of this blog, of which there are none, will no doubt have noticed the long gap since I last posted. I've generally been a fairly frequent poster, but it's been nearly two months since my last. Well, I've been busy. So, what has happened?

Northern Rock Cyclone: So, after a reasonable amount of training, I managed to do the middle distance race which was 62 miles long. If you add in the distance from my house to the start and back, this was 68 miles in one go. Okay, at 12 mph, it's a bit of a trundle, but I felt good about doing it. If I can speed things up a bit, then I might try for the 100 next year.

Brewery Demolition: I saw explosive demolition of the old Brewery. Had a great view from from over the road at St James' Park. On film, buildings always fall down majestically; the brewery wasn't like that. We heard to countdown from the security guy's radio, then there was a flash of deep red light from the bowels of the building. Then it fell down. No majestic collapse, the building just fell to the ground. The dust rose up and swirled around in the brisk wind. Finally, it cleared and there was a pile of rubble. Deeply scary.

InstantSOAP: This was my first independent research project. It was only a year long, but because of a big gap in the middle, it finally finished in a short while ago. I ended up doing a reasonble amount of the documentation for it, and I've started to repurpose it for my neuroinformatics project, Carmen. It's basically an easy way of doing web services; I have it doing R now. It's being trialed out in a user tutorial in a few weeks.

Houses: I've moved houses, and am now living in St Peters Wharf. It's really nice. It nestles in between the river, an industrial estate, a waste recovery centre (that's a tip to you and me), and Walker.

Bio-Ontologies: I'm on my way to Toronto for ISMB and my SIG, bio-ontologies. We've gone against the main conference this year and, yet, registrations are up. I feel good about this.

Anyway, with that lot combined I've been far to busy to write blog posts. Hopefully, they'll get a bit more regularly again.


Bob Brozman

It's been over 10 years since I last saw Bob Brozman; in this time, he's lost none of his prowess, and learnt a fair few new tunes. I think he's got more rhythmic as well.

He's a difficult musician in many ways; he changes rhythm a lot, his sense of humour is continual and a little strange; his musical tastes are getting to define the word eclectic. But, he's also engaging, entertaining and exciting to watch. It was a superb gig; I would be a fool if I left it 10 years again.

It was a strange gig also; I was faced with a difficult choice: Bob Brozman, a house party or a combined barbeque and eurovision night. In the end, I know that I made the right choice. What was interesting though, is that this is the first gig that I have been to for ages on my own; since I have moved up north to Newcastle, I've had the fortune to meet quite a few people with similar music tastes. Actually, I really enjoyed being solitary; that I was exhausted added to it; I almost slept in the interval; I became totally engrossed in the music, and lost a sense of self.

I'd not been to the Buddle arts centre in Wallsend before; but they have some stonking gigs coming up. I shall be there for more I think.


Bill Bug

I've just found out the terrible news that Bill Bug has died unexpectedly; this has come as a shock to the community. Bill was a phenomenon and the sort of person that you need in science; he was interested in everything, had ideas and opinions about it all, topped with an almost childlike pleasure in it all. He was a good scientist, a motivation and a reminder why most of us got into science in the first place.

His emails and their length were legendary. He was hard-work — you had to fight through the morass of ideas — but well worth it. I only had the pleasure of meeting him once; I was looking forward to meeting him again, something that now will never be.


NTFS Encryption

I decided that the time had finally come for me to encrypt the home space on my hard drive of my laptop in case it gets nicked; I've been encrypting high-value information for years, but I thought the time to just do the whole home space had come.

So last night, I set it going. It started off suggesting it would take 12 hours. Okay, no worries, I'd rather not leave the laptop overnight but needs must. By the time I left work it had dropped to 6 hours, all going swimmingly.

Get in this morning, look at the progress bar; 92 days remaining. Oh dear; I mean I know I have a lot of files, but there's only 10G of stuff there. Next stop, true crypt I guess.


Doing research

Yesterday was the board of studies. Day before was the board of examiners. Conclusion: today is the first day of summer, an opportunity to apply myself, mostly fulltime, to research.

So, what have I done today. Erm, teaching. Almost all day. Life can be hard at times.


Friends Re-United

Struck, no doubt, by the facebook phenomena, I noticed today that Friends Reunited has gone free. So I wrote to a couple of old friends whom mailed me 2 or 3 years ago, but who I was too tight-fisted to pay to reply to. The first has replied; turns out he's now a published author (I mean real books, in bookshops, rather than technical books), writing about murderers, werewolves and general ghost stories. He was always a talented bloke. I'm pleased he's now been unleashed on the world at large.


Toumani Diabate and Rachael Unthank

Last week, I saw Toumani Diabate at the Royal Northern College of Music. My experience of the Kora is a busker who plays in Manchester at times; he's pretty good actually. In concert, though it becomes a different instrument. The music is actually fairly repetitive, but the pieces generally play in cycles, flowing rather than jumping following one theme, then moving to another a note at time. As a result, it's hypnotic rather than exciting and lulls the audience. He only played four numbers (before the encore); I think that like many people, I was surprised to find that this had taken well clear of an hour.

The one negative part of the night was the accompanying blurb; this suggested that the audience should stiffle any sneezes or coughs and not open sweets during the performance to maximise everyones enjoyment. I mean what a load of po-faced nosense; like the SAGE, it's obvious that the RNCM is a snobbish, uptight venue but this is really taking it too far. Music is to be enjoyed, engaged in, not worshipped with great reverence. When I rule the world, I will find the idiot responsible for this statement, and string them up publicly, in front of an audience, to whom I shall allocated bubble gum, packets of crisp and low velocity, high volumn sneezing powder air rifles.

Rachael Unthank and the Winterset at The Round was the an entirely different experience. A small intimate venue anyway, they were playing on home turf; their mum (the two main singers are sisters) was in the audience. The venue is odd — basically someone's put a roof on the gap between two buildings. The sound proofing isn't too great; you could hear music and people walking upstairs, but this makes it more personal and engrossing. The music was wonderful; like much folk, and Toumani Diabete it's often hypnotic. Their arrangements are remarkable, often highly melodramatic, and very innovative especially when compared to more traditional folk. I think, we were lucky to get tickets; I'm not sure that they will be playing a venue that small in future or will sell out quicker than they did.

Wish she hadn't done the gag about Hexhamshire though; it was about a misheard lyric; I won't repeat it. I've had the song (Fareweel Regality) running through my head for the last week; now it will be associated with an alternative version instead.


Hardy upgrade

Moved my desktop to Hardy today. Had a few errors but it all went smoothy, right up to the point that I tried to use it, when I was getting lots of wierd stuff with the mouse. Basically, left click was giving double click events.

Took about an hour to work out; I'd configured xorg.conf a while back to enable mouse wheel emulation on my trackball. As a result, the upgrade didn't add the vital new line (Option: Core Pointer) without which it doesn't work.

X still sucks; the configuration is bizarre, unfriendly, inconsistent and impossible to debug. One day this will all get fixed. I hope it's soon.

Actually, thinking about it, the install balked have way through and asked me something, which was irritating as I was at lunch; unintended installs are good!


Dolls House and Battle of the Planets

Saw the Doll's house at the Northern Stage this week; it was well done, had some nice gags in it. But basically, it was dreary, long-winded and rather dull. I didn't like any of the characters, the central plot device was silly and I just wanted it to end. Right at the end, it perked up a bit, with the patronized woman, spreading her wings and starting anew; but, this felt unbelievable, and it makes no sense spending two and a half setting the scene for 5 minutes of excitement. I can see that the play must have been revolutionary at the time, but it now is only of historical interest.

Battle of the Planets, on the other hand, has little plot, doesn't really make sense, and is generally daft. But it's full of 70's haircuts, the animation is exciting and the score is wonderful. Added to this a chief baddie who wears red, thigh-length boots, a villanous cackle and the most fullsome pout this side of page 3 and you have a winner. The Doll's House has probably helped to change our world, redefine the relationship between men and women, and has last a 100 years. But BofP was more fun to watch and at 30 years old ain't doing bad either.


Junk calls, doctors and herbs

I had to take my car to KwikFit yesterday as my exhaut was hanging off by a thread; I was irritated to be phoned up by them the same day. How was the service, they asked? Could we have done anything better? Well, the exhaust hasn't falled off in the half mile from the garage to my house, and can you reduce the cost to 20 quid, please. Free would be better. Turns out they didn't care, they just wanted to try and flog me car insurance. No, you can't give me a quote, and no you can't call me back next year.

I've been reading "Medicine balls" by Phil Hammond; fine stuff. He repeats the old ear, nose and throat gag: never put anything in your ear small than your elbow. This makes me wonder, how to explain the stethoscope?

I've also added a new Silly idea. Only 6 months since the last; what a flood of ideas I am having?



Today is the kick-off meeting for ONDEX. This is a new project which is doing something that I've wanted to do for ages; in a nutshell, it's a large, graph-based datawarehouse. It's rather similar to a proposal that I wrote with Mark Wilkinson from BioMOBY a few years back, with one important difference — the system actually exists, produced at Rothamstead over the last few years.

The new project involves integrating some other bits of technology — taverna, text mining and so on, and a couple of specific biological examples. I think it's going to be a pretty cool project, and we should get some useful biology out of it.

Two things that I have learnt today: firstly, what "Ondex" actually stands for is not actually sure and, secondly, some varieties of willow are dodecaploid. Why would any plant need that many genomes?


Prat of the day

I've never stayed in the conference hotel at Manchester before. I was a little surprised to be kept away by a bunch of chortling idiots in the corridor at midnight last night. As a result I woke up pretty dazed, then almost brained myself on the handwash basin which has been clever placed in that part of space your head naturally inhabits while sitting on...well, I'm sure you can work it out.

It looked like the prize for prat of the day was going to go to room service. Leaving the floor mat over the edge of shower tray is not a great idea — most people turn the shower on before getting into it; how could this been beaten for being stupid?

Five minutes later, I took my spare pair of shoes out of my luggage in preparation for the new day. Both of them for my left foot. Hmmm.



Am in Manchester for an Ontogenesis meeting, which is focused on tools and APIs this time; perhaps less exciting than previous meetings, but also potentially most useful; spanners are not interesting, per se, but where would we be without them.

Sean Bechhofer started off talking about the OWL API — it's taken a long time, but this seems to have been a bit of a slow burn; it was started in 2002. It's starting to get a lot wider use now, and a bit of a community around it.


Night Listener and Northern Exposure

I have finally finished reading the Night Listener. I've always had a fragmented relationship with Armistead Maupin; I keep on getting half-way through a book, then stopping. I borrowed More Tales of the City from a friend, for example, and was half-way through reading it, when I found the copy I had bought 3 years before and then stopped. In that case, I had moved house in between and it got backed at the bottom. The Night Listener got caught by my move from Manchester. I've tried to start reading it again several times, but mostly while travelling; I think it's been around the world at least twice. For some reason, I picked it up a few days ago, and read the second half in two days. My conclusions: it's great, nicely paced, gentle and engrossing; the writer-writing-about-a-writer plot only annoys occasionally.

To celebrate my success in finishing it, I picked up Atonement, as I have stalled on this several times. Hmmm. Well, less good here. I still couldn't care less about Bryony's adolescent playwrite prentensions, nor understand why it needs so many chapters. Worse, I've read these chapters four times now. I should hire the film, but it's got Keira Knightly in; an actor that you can see through both metaphorically and physically.

I've been looking forward to the second season of Northern Exposure for a while; unfortunately, the music has been replaced with elevator musack. Moreover, as well as the music being badly chosen, it's been mixed poorly, at bad levels. It totally breaks the suspension of disbelief, making it's very hard to get involved. Very poor performance, indeed.


Wubi and Hardy

Installed Hardy Heron today on some laptops I have at home — I had decided to try and rip my entire CD collection again with consistent naming and organisation, and the best tool for the job — ripit — is linux based. The wonderous wubi makes a quick installation for a single purpose possible. There is not risk to your machine, and no painful partitioning to be done.

Hardy worked pretty well. X worked fine, as did the new resolution switchers. They have moved the location of the "no, no, no, don't autoplay the CD, not under any circumstances, just don't do it" dialog from removable devices and media to the file browser. They need to rename something—a CD is "removable media" in my book.

I couldn't get the wireless to work which was pretty disappointing, but this turned out to be because I had clicked the wrong button — if you single-click the network on the panel and pick the relevant network it all just works. If you right-click and fiddle with the settings yourself, it doesn't. Hardy actually got all three of my cards (spread between two computers) with no problems.

Neither computer is upto much, and each CD is taking ~20 mins, which is much longer than I expected. Still can't really blame hardy for this.


Worse lines ever

Went to see a for sale flat at the weekend. At one point, the estate agent said "I dreamt last night that I owned this flat; when I woke up and found that I didn't, I was devastated".

Really, it's true. I am not making this up.


Third Account

Yet another post has appeared about Ade Wolfson, this time from a parent of one of this kids, this time in the public media; it's could that a counter-opinion has appeared in the mainstream media: not everyone is internet-centric.



Just tried the BBC's iplayer for the first time. Pretty good, actually. It basically works, the image quality is good, download speed is fine. The download manager is pretty clunk and limited — you can't control how many things it downloads at once for instance. The DRM is a pain because you have to use windows media player to watch stuff back; normally I am a VLC man, and I miss having the keyboard shortcuts.

Shortly after downloading a few things, my download speed plummted. I think Virgin have chocked me for blowing my download limit, which is the first time this has happened. I managed to get a "0" reading on a download speed diagnostic; strangely, it also showed I have a 2MB upload which makes no sense at all. Is cable not asymmetric?


Take it all back. IPlayer installs kservice.exe as an automatic systems service. This spams the outgoing connection even after terminating iplayer. Moreover, it's a CPU hog, that turned my machine to treacle. This rather disingenuous blog post mentions the problem, says "it's outside the scope of this article" and suggests you firewall it out. I have a better idea; the BBC should switch the damn thing off. Very, very poor.


Second Account

A second account of the death of Ade Wolfson has appeared online now; I've never met the author, but it's a good write-up. More information in it than mine.


Gilberto Gil and Monica Vasconcelos

All a bit mad, having been on the road for a while, so just a quick review here. When he started, I thought he was well past his best; probably because he was singing in a strangulated falsetto when we got in.

Anyway, this turned out to be wrong; he was just warming up. The singing got better and the guitar was wonderfully rhythmic. Afterwards we squeezed into the little hall for Monica Vasconcelos, who played mellow jazz, and samba tinged music. Good voice, excellent band.

And all for 7 quid, in the cheap seats which I quite like. No complaints there.


Mermaids 2

Back in Copenhagen. Turns out I was wrong about the couched area — it's still there, just hidden behind the smoking room.

Trondheim was a lot of fun. I was there for a thesis defense. It's a lot more formal than in the UK; the candidate has to do two lectures (one on the thesis, one on a related topic that they find out two weeks before) and then they get a public examination. We were in a very impressive room, with two lecturns, like a court. The whole experience was a bit strange—there's a large degree of theatricality to it. On the whole, I think it's better than the UK one which consists of three people sitting in a room for 3 hours; it's rather anti-climatic, while the Norweigian version has a sense of occasion about it.

I have a theory, though, about feedback in science. It's well known that once you start to do well in science, then success breeds success; you get better known, more opportunities come your way and so on. I've been starting to wonder whether this is, in part, due to airports. The more successful scientists travel a lot (much more than I). The truth is, in this day and age, airports are great places to work. There is nothing else to do, laptop batteries last long enough. Travelling gives you intermittent access to the internet, so you can get what you need, but can't spend hours reading BBC News as a work-avoidance strategy. In the last few weeks, I've got lots of stuff done, as well as writing blog posts of course.

I am going to test this theory next week, by spending the entire time in the airport. Newcastle is only a 15 minutes from my house, so I plan to go up at 9 and sit on the concourse till 5. But will the magic still work if I don't have a valid ticket? I will report back.

Right, boarding...



I'm sitting in Copenhagen airport, next to the inevitable statue of the Little Mermaid, which resides between a lift shaft and a coffee shop. I'm travelling to Norway to do a thesis examination; I'm quite looking forward to it, to be honest, although I wish it wasn't in public to be honest.

I haven't been to Copenhagen since 2001, I think, when I was here for ISMB. The flight in was pretty bad: small plane, big bumps. My memories of the place are confirmed; it's a nice airport, airy and light. I have a veggie noodles which was actually pretty good. The nice balcony that I remember, on the first floor—low seats, lie down couches, free from children—now mostly houses the smoking and kiddies area (separate of course) and, so, has transformed from the most to least desirable part of the entire airport.

I would have loved to pop into Copenhagen itself—I seem to remember it's not far—but I have to re-read a thesis. What with the trip to Japan, I haven't had time to do it before, hence it's become an airport job.

I'm not doing my carbon quota any good here, about another 200kgs up in, well, whatever the combustion products of a plane are.


Now in Trondheim. I've never been so far North (well, not while on the ground). It disappointingly warm at -3C and there's not that much snow around either. Trondheim, from a drive through and brief wander, is cool (sorry). There's an amazing number of pubs (half of them are "British" — I've walked past "The three lions", "Little London" and "Macbeth" already; I'll leave you to work out which is the Scottish one. The street I am on, also has a curry house, a vietnamese and a chinese resturant. I could almost be at home, except for the unfeasibly steep angle on the roofs.

I'm also a new person from before. I've seen the Northern Lights. Not seen them well, I admit, through the window of the plane, with the reflection of a reading light in my eyes. But, I have always wanted to see them, I always knew that some day I would, and now I have.


The Biscuit Factory

Went to the biscuit factory yesterday for the first time. On the whole, it was pretty good, and I enjoyed it. Most of the stuff in there was wildly too expensive; they had a lovely mirror, for instance, with a carved wooden frame, but 700 quid is just too much for something that has a reasonable chance of getting broken.

One of the things that amused me, though, was the artists' statements. They seem to be required these days; people appear to judge art by what the artist is thinking rather than what they can see. I guess that they are teaching the writing of these personal statements in the art colleges nowadays; one thing that it is clear they are not teaching is grammar—in some cases it was terrible (okay, I hear you saying, maybe the pot is calling the kettle here, but blogs are quick written not studied).

These statements varied from the pretentious to the prosaic—with more of the former. A selection of my favourites (or paraphrases from memory) with my translations were:

  • the individual instintively views the piece from many different angles and viewpoints (translation: it's a shiny mirror and looks pretty in the lights).
  • the latest series explorers the artists emotional response to the weather on the bleak moorlands of Northumberia (translation: hell, it's windy up here).
  • "I dislike personal statements as they force the artist to move from the abstract and ambiguous realm of the medium, to the concrete realm of writing" (translation: I'm a painter! I like painting; I hate writing).

My favourite statement, though, was short and simple. It went

"Emma (I think this was her name) generally paints from the local environment. She paints from what she sees. She likes to work on location wherever possible as she enjoys the interaction with passers-by".

Wonderful; if she had replaced "enjoys the interaction" with "likes to natter" it would have been perfect; frank and to the point. The paintings were good as well.


Palace and Wastelands

We've had a series of good meetings, I got lots of chance to talk about metadata. It's clear to me that there is plenty of work to be done, but that it's starting to happen. It's not clear to me who will play what role, nor whether we will just repeat the history of bioinformatics. I guess neuroinformatics has the opportunity to do something new, ignore the legacy, that it could even avoid the pitfalls; having said that, one of the biggest pitfalls of bioinformatics was doing everything afresh without looking into the rest of the world.

Yesterday, I got a proper chance to do the tourism thing; we ended up in the electric district, partly by chance — Paul had a guide book, but the hotel wouldn't let us back into our rooms to retrieve it, so we have no above ground map. The electric district is, like the rest of Tokyo, an information overload but more so. At any time, you can here four or five recorded voices, there are flashing lights and music, and signs in Japanese and English everywhere. After that we went down to the palace gardens but they were shut by the time we got there. Evening was food with our ever gracious hosts; lovely again.

Back on the plane now, we are suspended above a Siberian wasteland. Perhaps 2km below, highlighted against the curve of the world there's another plane running parallel to our course. Another ton of carbon released into the air.


Film of the reverse Flight

Lions and Lambs — three interlocking stories, over the theme of war and the media. Well done, entertaining, and a light touch. Rather too earnest too eager for me. Lacking a bit in humour

We own the night — a cops and robbers flick, with added family drama. Not a bad film, although felt rather like Cagney and Lacey on steroids. Good performances all around, lots of brooding silences and a fortune spent on blood bags.

Beowulf — finished it off. Looked great, some wonderful hacking and slaying. Story was a variation of the original with (as noted previously) added masturbation gags. Turns out that the story was adapted by Neil Gaiman; explains a lot.

L'auberge rouge — a black, murder farce. Big ensemble cast, lots of fast dialogue, and pretty well done. Not nearly as good as Juno, but the best of the lot.

Juno — missed the first five minutes of this, so watched them as well, and then let it run on a bit. Strangely, it's been Japanese filtered on the way back; that is no swearing, no sexual references or, indeed, to any bodily functions; head-lopping and guns are okay, but sadly Juno is short on the latter.

Four and a bit films in one flight — well, I am tired and all the of the padding in my cushion has gone, and everything from my knees to sacrum is aching. And my shoulders and neck come to that.



So, this is my second time in Japan. It's slightly less confusing than the first; so far, we have been banging against one cliche after the other. It took us a little over an hour to get to the hotel from the airport; we got there at 11, to be told that the rooms would be available at 4pm. Exactly 4pm. So, we went into Tokyo and had lunch sitting on the floor — not good after a flight, I thought my knees were going to seize up. It was good, though, even managed to get something that was mostly veggie. We got back to the hotel at 3:40pm; we were directed to seats till 4pm, where upon the receptionist was prepared to give us the room keys which had been in the pidgeon holes behind her for the last 4 hours.

The hotel is basic but okay. The toilet has, disappointingly, only three controls: shower on, shower off and level. The latter controls the pressure of the cleaning jet which varies from gentle tinkle to colonic irrigation.

Evening was another meal. My eyes rolled when I saw another low table, but it was one which you could put your legs under. The meal was great and involved several varieties of sake.

Got back to the hotel at 9, and after many hours of being awake slept like a log.


CARMEN on Tour

Just given a talk at Riken about metadata. People seemed very positive, there is clearly a desire to do this and to get more data types out there. I got the question about requiring too much metadata to understand an experiment; most of the rest were people saying "have you thought about using...?".

The one that I hadn't thought about is provide metadata for gold standard, generated (non-experimental) data. My initial response is to say that we should be storing the service for producing the data, rather than the data, although there are purposes for standard generated data — enabling deterministic behaviour of tools over "random" data.


Google hits

Well, depressing though it has been, I'm pleased to say that I managed to get the forth hit on google, when searching with "Adrian Wolfson", alongside all the poor tabloid journalism.

In the end, I turned out to write quite a lot about his death. As well as the blog piece, I wrote some short words—I think that the plan is to put these into a book of remembrance. Depressingly, I am not going to be able to get to the funeral, as I am in Japan (actually I am over China now, on the way). I would have enjoyed meeting my friends again; truth be told, the chances that I will see most of them again are now very small. Ade was my main point of contact.

I don't think my remembrance is particularly good. I think the blog is far better, but I stick it up here anyway. Perhaps, it will help with the google hits.


Film of the Flight

Watched Enchanted, some of Beowulf and almost all of Juno.

Enchanted — a reverse fairy-tale, like a live action Shrek. Not bad, actually, kept me going for a while.

Beowulf — blood, guts and some serious beef swilling. Definately aimed at the adult market, containing at least one mastubration gag. Would probably have watched it, but the it was a bit dark and I couldn't hear the dialogue over the plane noise, so I stopped half way through.

Juno — a comedy about a teenage pregnancy. This was by far the best of the bunch. Quirky, funny, and beautifully acted. The whole thing is done without sentimentality (just like Enchanted, er...), but the characters were still wonderfully endearing.

I spent too much of the film trying to identify two of the actors (from the daredevil and spiderman films as it happens). Yeah, well, I'm on a plane and ache all over.



Not been to the Northern Stage, at least not for a show. I used to get food there sometimes, but it's expensive and the portions have got smaller.

Went to see Static last night. Strange thing — it was a cross between a music commercial, a mystery story and a tragedy. It's mostly about a woman coming to terms with the death of her husband. The side-plot is that he is deaf and the story of how he looses his hearing.

It was pretty good actually. I was dubious at the beginning; they used a lot of short sentances to the audience to set the scene which I found rather disjointed. But the story started to run after that. The "innovative staging" failed to detract from the story, the music was quite fun and the twist at the end worked pretty well. Worth going to see.


Little Things

Sometimes I feel that new technology is designed by perverse people, strictly for the purpose of raising negative emotions from the rest of us mortals. For example, I have a cordless phone in my house. My parents bought it for me a few years ago. It has worked flawlessly since, if I exclude losing the handset when the battery was already low; next time I needed it, the battery had totally gone so I couldn't use the "make it ring" function. Was 2 weeks before I found it—the laundry bin if you are interested.

The address book, however, seems designed for mockery. There's only space for 15 contacts. So this is what the designers think of me, that my social life is so miniscule that I only phone up 15 people? Worse, is the reality of the situation that I only have 11 numbers in it and, of these, one is phone banking (I'm scared of the internet) and the other is for recovering my mobile when I throw it in the laundry bin.

Now, though, it's got worse. The first entry is for Ade Wolfson, whose death I am still coming to terms with. I change the addressbook rarely enough (i.e. never), so that I've no idea how to remove the entry. It sits there, poking me everytime I make a call. This little thing seem cruel.

Perhaps, though, it cuts both ways. I remember my grandfather's funeral. It was summer, and a warm day. Inside the church was cool and pleasant. During the service, a butterfly fluttered around the pews, flying up to the ceiling. It was a beautiful moment. In an incredible act of irrationality, I couldn't help but think that this was my grandfather, flying away and it was comforting to me. Later, my brother talked about the butterfly; he'd been thinking the same thing.


More on laces

My last attempt to get a pair of shoe laces were met with some difficulties. It was, therefore, a source of distress to find that both of them broke, one after the other, in the same shoe, in a little more than a week; Timpson's have fallen of my Christmas card list as a result. So I then tried a second set. Four shoe shops before I finally found a set. These have now broken also.

So, today, I went out again. Schuh had only one pair for boots (thick as a phone cable, long enough to garotte an elephant) and one pair for formal wear (2 individual strands of polyester, topped with a bit of plastic). Clarks had only brown laces. The guy in John Lewis' shoe department said "well, I'd expect them to be around here". An older and wiser member of staff directed me downstairs, where a third pointed out the laces — "on the right, in the last fixture, just after the ironing boards".

I am now a proud owner of two pairs of black shoe laces, cost £1.20. Apparently, the manufacturers have been "in shoe care since 1911". I will report back; if this pair fails, I have decided, despite being a veggie, to go onto the town moor, slaughter one of the cattle and tan it's hide, from which I will fashion leather laces. I've now spent five quid on shoes laces for one shoe which is pretty old anyway. I realise this is taking the disposable society a little far, but perhaps they sell shoes for less than this.


For a friend

I've known Ade Wolfson for about 16 years now. In that time, he has been a good friend, a good colleague and a source of endless humour. Last week, he died. The facts of his death are a matter of public record: he killed himself, shortly after being charged with committing a sex act in front of a child. As I think about these facts again, that I have turned over in my mind many times, they still seem as strange and bizarre as the first time.

I met Ade while at University (or just shortly after). We worked together for a small charity, looking after children, providing them with a holiday, when they were unlikely to get another. Neither of us did this work out a sense of do-gooderism. For myself, I never really liked children that much, but I enjoyed the domesticity of running a holiday, as well as the sense of commonality of a bunch of young adults, struggling well outside of their experience to provide these holidays. Ade was much the same, except for the bit about not liking the children. He was a natural: he could settle the homesick, enthuse the recalcitrant, calm a pyscho-nutter. His story-telling was legendary within a year. It was no surprise when he became a school-teacher; anything else would have been a crime against his talents.

As we moved further away from University, we kept in touch, initially through the charity, and later for ourselves. We spoke infrequently but regularly. We both started to display a touch of Homer Simpsonness in our appearance, but other than that we had little in common. Being a school-teacher provided Ade with a gold-lined rut; he loved what he was doing, but worried that it would speed him toward middle age in his twenties. For myself, the insecurity and lack of responsibility of a contract research scientist threatened to keep me as an eighteen year old in my thirties. We spoke about this at times; other favorite topics were the state of his plumbing and Harry Potter; Ade had introduced me to Harry around book 3, while I was living in London. Over the next few years, we completed a post-modern analysis of the plot ahead of publication — for the record, he guessed about Dumbledore, while I got Sirius.

We saw each other rarely. I think the last time was nearly 5 years ago. He lived in south London; I consider the capital to be less habitable than Mars. We tried to hook up a few other times, but it didn't happen. I am left with a memory of him, a kind, wonderful man, with a great laugh and an overgrown beard which he had, in reality, long shaved-off.

His death is a tragedy and distressing to many of us who knew him. That such a straight-forward man should die in such melodrama is unfitting to say the least. That he chose not to defend himself, as I am sure that he could, that he could not find the support from all those who loved him, is painful to us all. But since I heard of his death on Saturday, I have also thought much of the time in his presence, of the stories we were part of, and the friends that we were. I've enjoyed re-living these memories more than I can say.

Adrian Wolfson, RIP.


Hugh Cornwell

Never seen him live, so thought, why not. Basically, he was okay. He has a substantial back catalogue, and is a powerful songwriter. But ultimately, he's not a great performer. He's witty and engaging, but neither his singing or guitar-playing is particularly fantastic. I found myself waiting for one of the big hits, and then being slightly disappointed by it; Golden Brown is needs more than a strummed acoustic.



I've been an avid user of fusesmb for a while. I found it to be very good, but a little hard to set up. For no readily apparent reason, it has stopped working for me.

So, now I am trying out sshfs instead. This worked better than fusesmb anyway — in particular directory listing was much quicker which was a real problem with fusesmb. However, I had a major problem which was that rsync did not work to a sshfs mounted directory. I got a wierd error about file renaming. This was a hassle — I use rsync quite a lot. In particular the —delete option is great for websites which I develop in one place, and publish to another.

Anyway, I found the solution today. Delightfully, it is this. Instead of mounting with sshfs, you add a new option to get sshfs -o workaround=rename. It's rare that you see such a honest command line...


Out of this world

I'd been saddended earlier by the closure of my local hippie-veggie shop, "OutOfThisWorld".

I was rather surprised therefore to walk into one in Beeston, Nottigham at the weekend. It turns out that the both this branch and the one in Leeds were bought by their managers from the parent company.

Good stuff! Hope that they do well. With any luck, they might expand. Newcastke might be a good place to go, as they are in need of a new hippie-veggie shop I hear.



I've been looking through the stats created by workrave. I'm slightly surprised to find that I make between 16 and 45,000 keystrokes per day (on my desktop at work — more if I include home). And around half a kilometre of mouse movement.

That's a lot.



I've been getting some needling recently for my grammar, spelling and composition, at least on these pages. There is clearly some justification for it. I normally have a relatively high standard for these things and, yet, these blog pages do fall below these standards.

Ultimately, the means of communication do affect how we behave; the blog feels more conversational, less formal. I tend to write this stuff out once, and rarely even proof-read it.

I shall think on this; my worry is that if I spend time improving the presentation, I might just not write anything at all. But then, if a jobs worth doing...



I was most entertained my Lord Falconers technically illiterate idea: that online news resources should remove prejudicial information about individuals during trials.

Pretty stupid idea. Apart from the technically difficult task of working out when a web page is about a particular individual, it seems to ignore the reality of the internet — that's is a global resource and British law does not affect it all. Asides from aggregator and archiving sites like, which would have to remove, and then reinstate potentially thousands of websites per day.

Suggesting that we pass new rules, attempting to put the genie back in the bottle, lacks any sense at all. Perhaps not a surprise from a judge.


Spring madness

Next week, I start teaching again. I've had to rewrite a practical for my microarray course, because genespring has totally changed (we used it in the past) and because I wanted to use something freely available which the students can use after our freebie license runs out.

It's been a lot of work. This has conspired with the early spring deadline for conference season; I am now in the review period for three conferences at once, including ISMB and haven't yet done a lot of work for Bio-Ontologies. Next week appears to be an "incredibly busy" week; I've just blocked out my entire diary with events.

Maybe there will be a miracle next week, and I shall be magically freed of work. Alternatively, maybe, google calendar will undergo a terrorist attack or, worse, a power cut which would have much the same impact.


Data Sharing in Neurosciences

There was much amusement in the CARMEN project today. The journal Neuroinformatics published what looked like an interesting article on data sharing.

Sadly, however, no one has been able to read it; it's a Springer article and none of us can read it because it's closed access and $32 to look at. A strange and ironic reflection on the state of data sharing.

Perhaps, is what the paper says. Data is Mine!


Immediately after posting this, I started writing some lecture notes. I have so far copied images of Northerns, Westerns and several kinds of immunofluorescence straight of the web, all legal, all thanks to the wonders of PLoS. It's even easy to attribute them because they have given all of the figures individual DOIs. Working in neuroinformatics is interesting and exciting, but it also helps to remind me how wonderful bioinformatics it is.


Black Gold

Black Gold is a documentary about the coffee trade. It's conclusions are not perhaps the most astonishing in the world — the coffee industry makes lots of money while most of the producers, particularly in Ethiopia, are not doing nearly as well. Still, perhaps, these are points that need making again and again. The role of the WTO and the trade policies of the first world are, perhaps, less obvious.

The documentary seems to have a got a new lease of life, more or less entirely due to Michael Moore. Unlike his work, or Supersize Me, Black Gold lacks a comedy turn to keep the interest going although the main protagonist, Tadesse Meskela, is engaging and charismatic.

The music and cinematography are both wonderful, though, making this a clear and compelling film. Well worth a look.


The Power of Facebook

I've had about 10 different sets of birthday greetings over the last day or two, which is very gratifying. Unfortunately, it's not actually my birthday. When I first created a facebook account, I put in a random date for my birthday, so I could get through the stupid forms as quick as possible. According, my birthday was yesterday and I am 29. To think that I missed out on the Golden Jubilee, the '76 drought and the Sex Pistols by so few years.

The funny thing is that I think I have had more birthday greetings than I have ever had in my entire life. Whether anyone will speak to me again, now that I have so cruely decieved them is open to question.


Sourceforge Marketplace

Well, I understand that they want to make some cash, but the sourceforge marketplace dialogue that keeps on popping up is quickly becoming more annoying that the Clippy.

Get rid of it. I only want to say go away once at most.


Organisational Chaos

I went to Fenwicks today to buy a set of shoe laces and a some nutcrackers — an eclectic mix, I'll grant you. Fenwicks is a department store which specialises in confusing geographical layouts. It's taken me quite a while now, but I do have some basic idea of the organisation there; when I first arrived at Newcastle, I used to get lost and once had to phone the fire brigade to come and rescue me, entering in the morning and leaving in the early evening.

Today, I went first to the kitchen section, forgetting that it now sells shoes, and that the toy department downstairs sells kitchenware. So, I popped downstairs to the toy department for the nutcrackers, came back upstairs to the kitchen department to get some shoe laces. Sadly, they didn't sell shoe laces — this would have been considered too logical and, therefore, against standard retail practice. Instead, they directed me to either the haberdashery department or the in-store Timpsons — people who cut keys and mend shoes. I decided against the haberdashers on the grounds that "haberdasher" is a stupid word. The Timpsons is to be found, straight-forwardly enough, in the food court, where I found the shoe laces (75cm, black, round). Sadly, Timpsons is not Fenwicks, even though the tills said "Fenwicks departments store", so while they could sell me the shoe laces, they couldn't sell me the nutcrackers. So, I walked through the sushi bar to the perfumeria which is convieniently located next to it (raw fish and perfume being natural bedfellows) and paid for the nutcrackers there.

The shoe laces are a bit short.


Rice again

After my last experience with rice, I decided to get straight-back in there. Bought some more, and cooked it with beans and stuff. Managed to overcook the rice, which I haven't done for a while.

I've been thinking about why I've started to each so many beans recently; then it came to me. I've got salad obsessed recently. My fridge is smaller than my freezer. Salad goes into the fridge, beans the freezer. It's all perfectly logical.


Rice no more

How the world has changed. Once upon a time, rice was my main staple. I used to eat tons of the stuff. Nowadays, I have a more varied staple diet: noodles, pasta, bread, wheat, cous-cous, rice and, of course, the occasional tattie. While I was cooking some rice last night, I noticed to my dismay that it had got some infection — small mites by the look of things which, fortunately float obviously on top of the water.

I've had a 10kg bag of rice in my house for most of my adult life, but I fear now that I have seen my last. I shall be buying 2kg bags in future.

The mites were incredible though; it's wonderful to me that a thing so small, smaller than this comma, can be a complete multi-cellular organism. Wonder what species they were?



I've started trying out Eclipse; I've decided to document my experiences as I thought that they might be interesting. Well, possibly. Possibly not. I'm just going to add to this as times goes on. So far, my conclusion? Pain in the backside.


The Inconvienient Insomnia

Got struck down last night with a major bout of insomnia. I was still awake at 4am, staring at the ceiling. I guess I was a bit stressed about work having come back from holiday last weekend, travelling a lot, and then straight to work.

In the end, I got up and watched my latest Amazon DVD; luckily it was light and breezy — An Inconvienient Truth. Actually, it was pretty good; wildly American-centric of course, although I guess the temperature graphs look more impressive in Farenheight as the numbers are so much larger.

This set me to thinking about my Christmas and New Year. Christmas was at Worcester, then I went to Tuscany for New Year. Most of the time, we stayed in an Agriturismo in Sinalunga. These agriturismo places don't have an equivalent in the UK; basically, you get a farm building, kitted out for living, on agricultural land. They get tax breaks so they can be pretty cheap. They are very popular because they help you get back to the rural idyll; at this time of year, this roughly translates as the freezing cold. So, we got through a ton of wood (literally) between 10 people for 5 days. Adding it all up in terms of fuel assuming the fuel is all carbon (wrong obviously).

Newcastle -> Worcester 15kg C (based on 20 litres consumption)
Birmingham -> Milan 55kg C (based on what it said on the plane door).
Milan -> Sinalunga 10kg C (shared with others, based on 30l).
Sinalunga -> Milan 10kg C
Milan -> Birmingham 55kg C
Worcester -> Newcstle 15kg C

Wood, 100kg (1 tonne by 10 people).
Kerosine 40kg

Makes a round 300kg of Carbon emited, or around 4 times my body weight (well, okay, 3.5 times then).

Which is about 1/30th of my Carbon footprint for this year, in two weeks, not including food and everything else.

What can I say? I was feeling much more relaxed about work stresses afterwards, so in a wierd way, I guess the film worked. I managed to get a whole 2 hours before I got up to give a lab meeting talk to four people.


New Year

Well, back in one piece and in Newcastle. The Claremont Tower is cold and dull. I have 300+ emails. I think I want to go back.


Abbrvs bad for helf

I found out about a fascinating report about abbreviations from BBC News. The practical upshot of it all is that medics commonly use abbreviations in their records, and traced back to a number of fatalaties when they were misunderstood.

Abbreviations have got a lot of history in medicine. In many cases, they were meant to be confusing: FLK (Funny Looking Kid) or NFN (Normal for Norfolk) were designed to express something that the doctor didn't want the patient from seeing.

The whole problem here is the user interface is wrong. The person writing the notes is trying to save themselves effort, to the detriment of the reader. What we really need is something better to interact with, which is quick to input the data but where the underlying representation is precise. Difficult to do with the paper and pens that most doctors still seem to use.

At the same time, I saw a blog post about Scrivener. This is a new form of word processor, which is attempting to consider the way that authors work. As a long term LaTeX user, I am somewhat isolated from the horror of word, but I can still appreciate the desire. To be dealt with by the application like an author rather than a typesetter is something that word has still failed on. Scrivener has features like a proper outlining and the ability to attach notes. LaTeX gets outlining right (word fails because most people use the physical style markups rather than the "heading" markups), but I love the synopsis idea that Scrivener has. Notes I currently do as comments in LaTeX but something better would be good.

The irony here, is that the problem is backward from the medical notes. The author wants to write much more than than the reader actually sees. Word is more scalable than 10 years ago, and has more fonts, but the user interface basically is the same. Perhaps it is time for a change?



I'm travelling today; got to Birmingham airport rather too early. Had the traditional bucket of coffee and slightly stale croissant from Costa coffee (forgot to ask for a small coffee; where do you get a stale croissant from at 6 in the morning?). As soon as I got through security, they decided to evacuate us from the depature lounge, and then let us back in again before we were out of the door.

Still, I managed to add to my Silly Ideas wiki for the first time in ages, so all is not lost.


Pan's Labyrinth

Been a long time since I have written anything here. I have been out since October, but I guess I've just been busy.

Pan's Labyrinth is a remarkable film, with the only negative point that I suspect the rest of the Christmas fayre will be downhill from here.

The story manages to mix a fairytale with the real world story of life under fascism. The two stories intertwine in a way which is a benefit to both. The imagery of the fantasy part are deft and visually stunning. The violence, pain and bravery of the real-world wonderfully acted and moving. Topped of with a beautiful score, the film couldn't have been bettered.


Vista and Picasa

Trying to help my dad out with his computer. I've come to the conclusion that Vista is a pig. It's slow as treacle, unless you turn off all the 3D nonsense which frankly doesn't do much anyway. It's not very stable. Norton anti-virus refused to identify itself to uninstall; when I finally worked it out, the uninstall took for ever. Eventually I had to reboot; it turned out to be because it was waiting for input from me from a dialog underneath the "uninstalling" progress bar. And I could not get it sharing files despite my best attempts. The only nice thing — it knew the name of my router and opened up a browser to automatically.

Picasa is also a pig. The UI is slow, the scrolling uncontrollable. I want to add captions and place into an export folder but, unaccountablly, this takes about 20 clicks. Urrgh.


Christmas Parties

Amasingly I have nearly got to Christmas with no parties. I've missed everyone, two to being away at the FuGE workshop, or in Nancy. The last I missed because I have spent the last few days culturing bacteria in my throat, a traditional occupation at this time of year.



Just got a new Plantronics Discovery 510 — this is a bluetooth earpiece that I thought would be good for travelling; no wires to get broken and tangled up in my bag. This is the third device I recieved from Plantronics. The first two, Discovery 340 I think, were both broken. I think it was a systemic fault in the manufacture as they both failed in exactly the same way, during pairing. The 510 is a nicer device (sold at three times the price so that's not surprising). The main advantage, however, is that it actually works which is a relief. The sound quality is not that great though. I guess most people are using this over a mobile where you wouldn't notice, while the drop from normal skype quality is clear. Still, it will be useful, so long as it doesn't break.

Meanwhile, my new Virgin Broadband sufffered it's first outage. Around 18 hours, no connection, no DHCP, no DNS. Pathetic. Their authomated phone support service said "Some people may be having issues, and our engineers are working on it. Turn your modem off and on may fix it". Gods, talk about lack of specifics.



In Manchester for a FuGE workshop. It's a bit surprising actually, but half of Newcastle seems to have decamped down here. So far the discussions have been deep and intense; we established early on that it's pronounced "fugue". Everyone has ignored this and carried on pronouncing it how they started off. Personally I am fond of "fug-ee".

The University is a building site; I did see a patch of grass on the way from the station, but a guy with a theodolite was eyeing it up. The hideous maths tower is now a distant memory to be replaced by the scan building. This has been lovingly architected to evoke images of a gasometer. It's hideous.

Manchester seems much the same as before with a few shops gone, a few more appeared. Next to the stationary shop in the precinct, they have a Brazillian eyebrow plucking emporium; I think I may pop in tomorrow.

For food, we went to "No 4 Dine and Wine" in Didsbury; despite the silly name, it's nice. Quite homey and comfortable, the food was well-prepared and straight-forward enough, except for a tendency to balance the meat on top of the vegetables. The veggie options were okay; the roast vegetable soup was particularly good, although too hot; I ended up flushing burnt bits of the roof of my mouth down the sink at half time.

Surely the roof of your mouth should really be called the ceiling of your mouth?

Travel there and back was a pain. On the way, we couldn't get a taxi for love nor money (actually, we only tried money). In the end, we took the bus. On the way back, the taxi arrived okay, but he bought us back via Liverpool. "This is Oxford Road" he announced just north of Rusholme. Yes, I know. That would be the road we started off on. Eventually we got back to the Business School which has a 101 integrated hotel and sauna rooms.

My laptop fan is starting to make pained noises as the machine overheats. Time to sleep.


Flip side of the Coin

Well, now the flip side of the coin. Eurostar is late; first their excuse was mechanical failure, then security issues. Standard sort of nonsense that travel companies give. The last train for Newcastle leaves in 1 hour and I'm still in France. So, looks like a night in London, and guess the hotel is going to come out of my budget. I was kind of hoping to sleep in my own bed tonight as well.


Got it in the end, by about 1 minute. The run almost killed me though.


Social Events

Last night we had the conference social, which involved a trip to the museum. I grabbed a croissant and apple turnover on the way which was fortunate; I was very hungry by the end.

The Musee Lorraine is not huge, but well kept with a nice garden the middle. There were two tours on offer: the permanent collection and a temporary exhibition on glass. The tour guide was using English for the first time on a tour; she lost some words, accented others and was occasionally confusing, but was so enthusiastic, excited and expressive she more than made up for it. The exhibition was small, but good, showing the changes in glass from Roman times to the last century and, in parallel, some of the processes involved in glass manufacture.

Stopped off for (more) Italian food on the way home; the starter was good (tomato and aubergine bruschetta) and better than the main which was a little uninspired.

On the way home, workmen were putting up Christmas lights in Stanislas place, with a (slightly naff) igloo underneath.



I've just given my laptop a good clean out, in particular removing services I don't use. Killing Zone Alarm and VMWare has together had a massive impact. Previously, the boot took about one and a half minutes, and then after login there was another two minutes before I could actually use the system. The boot is about the same time, but I can use the system in 5 seconds now. Makes a big difference at a conference, where you hibernate and wake a lot.


Political Correctness Gone Mad

I'm all in favour of being nice to foreigners, but I think that it's all gone too far myself. We are now being so nice to people from other countries that we are making life harder for decent, hard-working British people.

For the last few days, every time I go to or, the stupid interface talks to me in French. Just because I am in France. Well, I think that this is just wrong. These websites should be in English everywhere. If the French want to be spoken to in their own language, then they should click a button or set a preference or something.

Anyone know how to stop these and other sites stop being clever and doing the wrong thing while trying to do the right thing?


Nancy by Day

Talk over; it went okay, I think, and I got a reasonable number of questions about some of my more provocative points, which is nice. I think that the talk itself could have done with a more clearly demarcated set of conclusions than it had; it needed a little more work and thought, but I just haven't had the time recently to do it.

Afterwards, I went to the workshop on accessibility. It was interesting, although it reminded a little of the microarray section of ISMB a few years ago; everyone was comparing their system to the gold standard (a system someone else came up with a few years previously). Unfortunately, I was too tired to pay real attention, so I left after the coffee break, and walked a few kilometres back to the hotel, in need of fresh air.

Nancy turns out to be a pleasant place, unrelated to the rain-sodden, weeping moorland that it was last night. Most of the city is tenement blocks; it reminds me of Edinburgh although with surfaced walls, rather than the granite hardness of Edinburgh's stones. The city is currently dripping with lights — testimony to the festival of St. Nicholas that has just gone, rather than Christmas per se. Unlike Newcastle, these are not confined to a few streets in the centre but are everywhere; if someone pulled the plug on main street lights, the whole city would still glow. It's quiet here at night, although perhaps that is just monday.

We reached INRA and the University by tram (actually a trolley-bus, with a guide rail most of the way) reasonably efficiently although they had suffered a breakdown that morning. The campus is strange — the architect clearly has a pathological hatred of right angles, circular buildings surrounded by curving roads.

The food has been, how should I put it, equivocal so far. I knew I was in for a veggie disaster at the restaurant last night, as the waiter uncovered my dish, with a flourish and a "Voila!" to reveal a plate of boiled vegetables. Meat course, without the meat. Lunch today was similar (the lentil salad, sneakily, included beef). Despite this, it's clear that general standard of food has been good; lunch was three courses, with wine; coffee came with a small cake or croissant, was strong, pleasant and in small cups; enough to stimulate without concomitant bladder problems. I won't criticise the cooks for not catering for hippie veggies given that they cook well for others.

Tonight, though, I went for the inevitable Italian meal. "Vegetarian pizza" said the waitress (en Anglais) "with red wine", with just enough of a hint of derision to make me feel warm and in France.


Nancy by Train

Today I am heading of to WebDIM4LS in Nancy, where I am giving a talk. Although I am really looking forward to the conference and the talk, it has been stressing me out a fair bit. I like writing talks, getting slides together, working out a good story—I hope that I have achieved it in this case—but things have been really busy at work, especially with the end of term coming up. I've found myself really pushed to find time to write it. In the end, I finished writing yesterday (that's a saturday!) at 8ish.

I'm travelling to Nancy the whole way to train, using Eurostar. I'd left it all rather late in booking travel, put managed to get tickets the whole way. It's very expensive; >£200, plus Newcastle to London at another $100. I think I could have got it for around 100, if I had booked earlier. As it happens, it was no more expensive than flying, though again that would have been cheaper earlier. Still, I'm quite looking forward to it. The tunnel is a new experience for me.

Out of the last four journeys I have made, I have lost my luggage in Paris, De Gaulle three times (the fourth time I lost my luggage elsewhere), so travelling by train seemed attractive. So far, it's working out well. The train is, well, more civilised than a plane. There's little in the way of through ticketting though; I'm conscious that a delay could mean the entire thing falling over. As we're currently crawling along to overtake a broken down train, this seems distinctly possible.

14:00 GMT

Well, the train was late, but I had enough time for the change over, and am now sitting in the Eurostar. Coming into King's Cross was a big advantage — Paddington or Euston would have been much less convienient. The St Pancras terminal is fine — security and passport control were quick and no hassle (wey, hey, you can take liquids). The waiting area is comfortable and heated. Boarding straightforward (although the coach numbers are hidden away on a LCD screen which really does not stand out). Looking around and judging by the large number of fat men in suits, it would appear that I am in business class, which is a bit of a surprise. Perhaps, this is one of the reasons it was so expensive.

14:15 GMT

The train's now moving. It's very smooth but looking outside, it's pretty clear that the train is tanking along. Definately in first class; just had a drink, and now they are bring around a menu.

I think that the power supply keeps getting cut though — my computer is switching on and off between low and high power mode. Either that or it's about to break.



Well, RSSFwd works pretty well, but it's often has a really slow interface which can be a pain if you want to change, for example, from HTML to normal email. So I'm giving RSS2Email a go. No support for OPML unfortunately, but it seems to work otherwise.


Closing Down

The two marks of being middle class have to be an overriding concern with house prices and strongly held opinions on the relative merits of supermarkets. I find myself distressed to write this post, therefore.

I've been a big fan of Out of this World since I got to Newcastle. The small, packed high organic shop that was here when I arrived re-opened last year as a bigger, more spacious place. Of course, it had plenty of terribly worthy food; food that you could eat with a clear conscience but without that much enjoyment. But it also had a lot of great stuff; the fruit and veg section was pretty good. The dried fruit and nut selection probably the best that I have seen. I was particularly fond of the dried mango slices.

Today, however, I've found that it is shutting down. I suspect that they over-expanded; as well as the new location here, they have opened a new store in York. Then, they've also been hit by the new Sainsburies which opened next door (ironically over the site of their old store). As well as having a bigger range, Sainsbury's is open for longer, including Sundays, and has free parking. It's an old story, and not a surprise; I was just waiting for the time. I can't help but be depressed, though, that the three rows of wierd things, of strange grains that you have never heard of, their bank of honeys from different parts of the UK, have been replaced by three rows of ready-meal uniformity.

Still, look on the bright side, combined with decline of Northern Rock (also based in Gosforth), perhaps it will mean a drop in local house prices.


6th Time

Oops. Just realised that Windows installed onto D, rather than C. So, yet another reinstall on monday.

This is harder work than you might hope. I've installed windows maybe 40 times. It shouldn't be hard.


Proof at Last

Yes, people do actually read this. Daniel Schober today wrote to me to point out an error in my post about bio-ontologies. I did a life blog, on a computer resting on my stomach while not jumping up and down chairing the session. I reported Daniel's post as "11:51 Daniel Schober is not describing efforts to standardise..."

I've now fixed the "not" to "now". Oops.


Reinstalling Windows

On my fifth attempt to reinstall windows now. Keep on managing to get something wrong — getting the hard drive partitions backwards or whatever. Also the on the disk format option it has "do you want me to do it quick, or to take ages". I keep on getting the wrong one and there's no way to stop it.

It even tells you "Windows will now format you life; Press Enter to continue" before it starts. And YOU CAN'T GO BACK! IT'S FOREVER!



Stress and Video's

I've been thinking about new mechanisms for teaching for a while; a post from Savas spurred me into thinking about it more; basically, I've come to the conclusion that lectures are boring for both the students and the lecturer. I was thinking to replace them with some funky form of website; rather like the ones that I do for practical classes, but with more content and less working through.

I asked my students about it. About half of them thought it was a good idea, half bad. The main concerns were whether it was going to be more work and more time sitting at a computer reading a website. Good points both. I think that the more work concern may be misguided, though, as it's based on the amount of stuff they learn in the practical classes; it's nowhere as much as they learn in a lecture although the knowledge is deeper. Others thought it was a good idea; most probably the ones bored of my rambling anecdotes.

I've decided that I am thinking too much though. This time of the year is stupidly busy; my mind tends to be constantly active. It's good in some ways, but bad in others. I'm not stressed about it, as I'm used to it, but my mind tends to flit backwards and forwards and I find it hard to relax; even when I am not thinking about work I think about other things.

I think this was responsible for the mini-nightmare I had last night; I'm not a heavy dreamer; I rarely remember them and when I do they are not the technicolour with stereo sound that other people report. Anyway, in this dream I had to travel to Edinburgh for some reason. So, I got the boat up (look, it's a dream, it's not meant to make sense). The trip up went fine, but on the way back it was a disaster and I lost my luggage; I woke up pretty suddenly and really stressed. Ah, the sad mundanity of my life.


Virgin Arrives

Just got cable fitted. This is the second attempt; first time the engineer didn't show up, or said he did, but didn't try phoning or anything. Wasn't too bad, although took quite a while and I couldn't use my existing extension line as I hoped. Think he should have vacuumed the floor afterwards, though, and was not best pleased to find that he left wall staples on my bedroom floor; would have been more than not best pleased if I had got them in my foot. All seems to be working, though.

Just unplugged my fan, and plugged in my office heater. Winter is here.



Well, the flight over involved an unexpected stopover in JFK; the ticket said "Salt Lake City" to "Paris", with a single flight number. Randomly this single flight involved flying to JFK, getting off, and getting on a different plane. I'm not sure in quite what sense this can be considered to be a single flight then. Never been to JFK before; previously, I thought that LHR was the worst airport that I have been to. It's not.

The actual flight was fine; had a interesting discussion with a woman from Puerto Rica. I confess not to know that much about it and about it's relationship with the US. It's clear that the country has some difficult decisions ahead.

Sadly, we got stuck in traffic at JFK and were over an hour taking off, so now I have missed my flight and am stuck in Paris for another 2 hours before I head for LHR. Three bad airports in a row. For those of you who are counting, this means 5 flights for one journey.

It's 1 in the afternoon and I feel bad.


Northern Exposure

It's 5 in the morning, and I feel fine.

I guess it's odd to be talking about Northern Exposure when I am somewhere South of Paris, but this is where is was filmed and it's does get pretty cold up here in winter.

I've never been much in the way for tourism, so a trip up to Roslyn, the physical location for Cicely, Alaska seemed like a pretty daft idea, but sometimes you have to just go with these feelings. Cliff was kind enough to offer to drive me up there. The trip there was, well, flat then hilly. The dividing line between the desert and the trees is really quite sharp. It's maybe a mile from the first tree to the full out forest. Once you get to the forest, it really starts to look like Northern Exposure territory.

We got into Roslyn late; we'd stopped for a quick lunch which had taken ages, after they lost the ticket (the offered us a free starter, but Cliff just got his cash back instead). The sun was still up, but there wasn't much left. The town is tiny, but relatively compact — no urban sprawl here. There is a central road running through it, which is actually at right angles to what appears to be the main road on TV. In the fading sunlight, the place was beautiful; lots of wood construction everywhere, peaceful and with the intense smell of coniferous wood smoke everywhere.

The effects of Northern Exposure can be seen on the town, but only in a small way. Joel Fleischman's office is now the Cicely Alaska museum. Just over the road is the corner store and at the bottom, the Brick. The famous mural is, as it says, on the wall of Roslyn('s) Cafe, rather than the Brick which is the impression that you get. The Cafe, as far as I can tell, is not featured beyond the mural. KHBR radio is just over the other side of the main road; it's still there with Minnifield Communications network up on the door. We stopped for dinner (veggie burger and fries) in the Brick; inside it bears little resemblance to the TV version; it's much, much bigger than it appears, has a stage and long bar, and a big log stove in the corner. I guess that the interior shots are actually studio based, and not here at all.

The town itself is much as it appears to on TV. But there is more to it. It's mining heritage is lost on TV (which would have placed it in the wrong area). The museum they had there was wonderful. As well as the camel mural, there are several others, including celebrating Roslyn's past. And just outside KHBR radio is an "war" memorial to those who lost their lives in the mining industry. I like these small towns; I could have happily spent a couple of days there, hung over, drank beer, drove (or walked!) up some trails.

The experience of being a dumb fan-boy tourist was a little uncomfortable for me, and combined with the declining day light, I didn't quite get the pictures I wanted (forgot to take on of the doctors office), so I'll have to go back another time.

It was a strange way to spend a day, but it was a quintessential American experience. Spudnuts and coffee to start (you may view the spudnuts here, but please prepare yourself first — it's not pretty). At lunch, we got fast food, and I got to see Cliff complain (no one complains like an American), then we drove for hours for little readily apparent purpose, to a place where I took lots of photos of nothing apparent. Wonderful.


In the desert

Yesterday I gave a talk at PNNL. It went fine, got a few laughs, had some interesting discussions about infrastructure for bioinformatics, and some new uses for ontologies.

PNNL is in Washington State, in Pasco. There are hills between here and the coast, so none of Seattle's rain gets here — basically, it's a desert. The cities have the classic urban sprawl; there is no city centre or down town area, just lots of roads with malls hanging off them. The roads are all about 16 lanes wide, with no cars on them. Space is cheap here; it took me 5 minutes to walk from the guest house, across the largely empty parking lot to the badging office. Unlike Livermore where I have been before, the security is relatively low key; no marine with a basooka strapped to his shoulder wishing you a nice day on the entrance here. They did give me a 30 page "visitor orientation" book. Page 1 says "look after the environment", page 2 says "don't drive too fast", page 3 says "no alcohol, cameras are restricted and wear your badge". From page 4 onwards, it's all about radiological safety including a section cryptically entitled "What about pregnant women".

I'm staying in the PNNL guesthouse, as they are not allowed to put you up anywhere else. They provide a complementary breakfast of microwavable muesli bars, and a 150ml can of apple juice (made from concentrate), which are replaced every monday. The sign telling me all this also says "enjoy your breakfast" which seems a tad optimistic.

The local delicacy here are "spudnuts" — I now said or written this word about 15 times and still find it funny. Basically these are doughnuts made of, well, potatoes. Despite being a desert, Washington state is also starting to make inroads into wines — you can see the vineyards from overhead as you come in.

Today, after a breakfast of spudnuts and coffee my host, the ever gracious Cliff Joslyn is taking me up at Roslyn — better known as Cicely, Alaska, home of Northern Exposure. I expect it's going to be pointless — there many be three buildings I recognise, or there may not. Hopefully, I'll get some reasonably views of the hills as well, rather than miles and miles of flat, brown and probably radioactive dirt.


Actually, it was pretty cool.


Too Hot

Last night we went for a curry in San Diego. The waitress (sorry, our Server for the Evening) asked me whether I want my curry "mild, medium, spicy or very spicy". Well, okay, very spicy I said (had a bit of a cold, so it seemed the sensible thing). She looked dubious; "I wouldn't advise that", she said, "why not have the spicy just to be safe".

The curry was nice, if bland.

Today I've flown into Salt Lake city. From the air, it's astonishing, with the white plains contrasting with the deep blue of the water. Apart from that, it looks like an bit of an industrial dump to be honest.


On a mission

Last night I came to an amazing discovery; the TV in the US can be great. Last night, I fall across UCSD TV. I watched a great lecture on the sociology of the stem cell debate which was most illumiating. I then stayed awake a bit too long listening to a programme on sleep deprivation and the body clock. University TV — a great idea. Perhaps Newcastle should start pod-casting — a daily lecture on some topic being researched or taught at the Unversity. Perhaps surprisingly, the straight lecture format works quite well on the box, and it's relatively cheap.

Walked around Mission Bay these morning. In the morning, there was a mist over the sky, the air was sweet with the smell of tropical trees and and heady with petrol fumes. It's a naturally beautiful area; I can't help thinking that it's natural beauty could have been enchanced if the city were not designed for the convienience of cars.

Wasn't sure what to eat; ended up getting Japanese — had edamame and veggie teriyaki; 10 dollars, large enough to feed a water buffalo who hadn't eaten for several days. Would have been nicer half the size and done better, but it was still good.


An apple a day keeps the Airplane away.

I'm flying out to San Diego today. I was sure that I was going to miss the connection from Cincinatti to San Diego after lots of delays with the flight. I managed to clear customs in about 5 minutes which is the fastest time ever, with around 20 minutes to go. But then I got stopped after a dog smelt apple on my bag, which I'd eaten on the plane, and lost another 5 minutes on another x-ray. Finally got to the gate, after a cross-terminal dash, risking life and limb rather than doing up my shoe laces. 3 minutes later the plane left. Fun actually. Haven't had to run across an airport for years.

Got loads of work done on the way, much of which has been hanging around for ages, including part 2 of a view of my Italy trip . I have to say that at least part of this is the lack of internet connection. Also, today I got up at 4am and the day is 32 hours long. Maybe that has something to do with it. I should travel more often.



I've been trying Before this I used which was okay, but seemed to fail for a lot of feeds. I like Google Reader, but having to go to a different application for just RSS is a pain. I was going for weeks without looking at it. So I am trying email again. It seems to be working for the moment; it has an non HTML layout and (seems) to be able to cope with all the feeds I use.


Rennie MacIntosh

Was in the Rennie MacIntosh hotel in Glasgow last night. It was a little bit shabby, but not too bad. However, the toilet smelt like they cleaned it with a dead badger. They seemed to have plumbed the shower waste pipe in after the toilet U-bend and the smells came up that way. I couldn't work out why the sewage itself didn't come up also, but it didn't; we should be grateful for small blessings, I suppose.

While I am thinking about it, I've decided to release chapter 1 of my treatise on Italy following my holiday there. I was going to release everything at once, but I haven't found time to write more; so here goes the first.



Woke up this morning (duh, duh, duh, de) to the sound of scratching from outside my window. The first frost of winter was spreading it's chill fingers over Newcastle. And some sod was trying to clear their windscreen at 7 in the morning.

A short while later, I walked out of my house, got onto my bike and rode off. Didn't even have to clean my glasses.


Acrobat Reader

Guys, this is a PDF tool. Why on earth would I need an RSS reader? I mean, what is the point of that? I already have an RSS reader. I just want to read PDF files, nothing more, nothing less.


Start the Week with Craig Venter

Craig Venter was on the start the week. I meant to miss it, but ended up listening by random chance. It was strange; he was thoughtful, understated, entirely reasonable and only talk about how great he was once. Unexpected to say the least.


Upside Down

Just put a DVD upside down into my windows machine (there were no labels on it, so this was not hard). Windows hung, then told me explorer was not responding, then killed itself, then rebooted. Impressive.


Jim Watson

I was going to see him talk on Sunday at Newcastle but it turns out that he's gone home instead. I'm reasonably irritated about this to be honest. I mean, I know he keeps on coming out with these daft statements, but I was going to see hear what he had to say; more just to experience a piece of history. Maybe a bit pathetic, but his work has helped to define my own working life and it would have been good to see it.

There seems to be a theme running along here. I was hoping to see Bo Diddley earlier this year but then he had a stroke.


Leather and Chrome

Richard Thompson — excellent as always, sold out the Sage again.

I've realised now why I prefer his solo shows to his band shows. As he sells out, he always plays big venues like the Sage which are, basically, horrible. To enjoy a band gig, you need to stand up and dance; failing this jigging about from side to side would work. The best band gig I went to was in Edinburgh; half way through I went to the loo, then spent the rest of the gig standing up at the back and had a great time.

Throw out the chairs!



Had to kill this on Ubuntu also. It's eating my entire disk IO all the time making it not very usuable. For the moment, I've just tried turning off the "watching" and left "indexing" on.

I don't know what "watching" or "indexing" actually does. I'm not impressed; this is not windows; having a nice GUI does not mean that you don't have to write technical documentation.


Dave Cowan's leaving do

Last week I went to Dave Cowan's leaving do. No idea who he was, but he decided to get Jess Klein to play. Kindly, he decided to open up the gig to the public which included me.

Jess was excellent again, better than the Cluny I would say. The gig was in the Black Swan centre which I've not been too, and the sound is far better than the Cluny with it's odd shape.

Had a talk with Jess afterwards; I'd had a few pints by this time so I wittered inconsequentially. Ah, well, I guess that she is used to it.


Updated to Gutsy

A Vmware upgrade didn't work for me. So I decided to update to Gutsy, the new version of Ubuntu. It mostly worked. Texlive was problematic, but I tracked this down to a copy of language.dat in my TEXINPUTS. Installing from a root console would have solved it, but in the end I just deleted language.dat which shouldn't have been there. Everything else worked straight away, no worries.

Well, except for Xorg of course. It didn't get the widescreen working, nor the track ball scroll wheel emulation. I had to hack the config file by hand. One day, this will all work, but not yet.



One of my bike tyres exploded last night. Rather unusual — in fact, I've never had it happen before. The side wall was a bit knackered. It's loosened from the bead, which slipped off, and the tube went bang. At 100PSI (I haven't gone metric for pressure measures yet!) that's quite a bang. My ear took an hour or two to stop ringing.

Sadly this was just after I finished changing the tube which was, therefore, brand new. Pain.


Backups are great

I reinstituted incremental backups a few days ago. I have a nice, new, big hard-drive now, so I thought why not. My data is actually copied to quite a few machines, so having a backup on the same hard drive as the data is less of a problem that it seems.

Anyway, a few days later, for the first time in ages, I found today that I had deleted a file I really, really needed but was able to recover it. Let this be a lesson. Backups are good.


Fusesmb again and Encfs

I did get this working in the end. Basically, my /etc/samba/smb.conf was wrong and needed fiddling with; gnome even provides a GUI for doing this ("Shared Folders"). Setting the domain and the WINS server and everything works.

Fusesmb is great; I have now symlinked in the machines that I want. It only seems to understand paths like //CAMPUS/machine_name/share which is a bit of a pain; paths like //internal/web which work within CS don't work here. I had to find the machine names by ls-lR'ing through the entirety of SMB space. It's also very slow, so listing directories with a symlink to an SMB location can be a pain.

But, given all of this, it's still great. Having a mount at the file system level rather than in the GUI works well for me. I have command line access, it works in Emacs, I can just forget about it and go about my work.

I've also tried encfs, which is encrypted fuse mounted filesystem backed by a "real" file system. Also, straightforward and works like a dream. One satisfied customer.



Well, I was not quite right. Hero does have a story, and it's reasonably engaging, although seems to be an allegory which says that the end justifies the means. Visually beautiful, well, yes, got that bit right.


Lots of Art

Lots of art this week. First Blowup, being shown to mark Antonioni's death (he was the director; fraid I'd never heard of him). Not a bad film. Wikipedia says that it "does not follow a conventional narrative structure", which I interpret as it not having a plot. Most of the plot seems to involve unlikely situations which allow for lots of strange angles and artistic shots, with 60s stylism to the fore. Still, the shots were very artistic, which was fun in itself. It's not aged well, but it's an interesting historical view.

The Alvin Ailey dance company played at the Royal Theatre. It started off with a dark and meaningful dance about something, backed with orchestral music and then moved towarded a more dancable (er...) gospel set which got everyone tapping. The dancing wasn't the best I've seen; the acrobat dance wasn't that acrobatic, the grace was evident but not excellent. But it kept me happy for the 2 hour show (with two long interevals!).

24-7 is another Shane Meadows. More engaging than This is England, but with similar territory. Bob Hoskins as a likeble boxing coach, with a dark ending to keep up the griity realism. I like Shane Meadows; although his films have a dark edge, he's got a great sense of humour which is never partronising, warm to his subjects.

Going to watch "Hero" now. Based on previous similar films, I suspect it's going to be visually beautiful without much plot.



Trying this out today. Not working either. I think at heart it's my SMB configuration that is hosed rather than anything else.


Autofs and others

Now trying out autofs — the cifs filesystems don't umount cleanly and autofs seemed like a nicer solution. Anyway, it looks like it's working — autofs and mount all show the right thing — but I can't cd into the directory.

One of the things that I liked most about windows, which I can't get to work under linux is start or from cygwin cygstart — which does all the right things with paths. Basically, it means "do the right thing with this file"; so start hello.txt will open hello.txt in Notepad or Emacs. On linux nautilus . works for directories but fails for files.


Told a lie

Today was no end of hassle as I tried to get SMB shares mounted — the problem here seems to be that it needs IP numbers; then I tried to get latex installed — tetex is broken, as you need to put the main directory in TEXINPUTS, TeXLive just doesn't install; and finally a recurring problem with vmware server which I think I have solved (removing vmware player services), but won't know till the reboot. Hmmm.


Back from Holiday, Linuxed up

I took the advantage of having not being in the middle of anything as a result of coming back from holiday to move to linux, and am not typing this on Ubuntu. A few things to do yet — not least getting my website generation working, so this blog may appear several days after I type it.

It's all gone reasonably smoothly so far. Took lots of running of unison. Got my email running today; some 350 mails in main box, with around 1000 in total (plus another 2000 spam). Hmmm, lots to read.


This is England

This is England is a classic British film; set sometime in the past, funny and full of gritty realism. It's beautifully shot, evocative and moving; although, it's about a bunch of violent racist skin heads, there is no real black and white (er, if you know what I mean). The film is warm and engaging.

I guess, though, I was always going to be a sucker for this. How could I not be moved? It was set against the backdrop of the Falklands, unemployment, Thatchers England. It was set against part of my childhood, set against my political awakening.

So, I didn't enjoy, but I am glad to have been. It's important to remember that time.



And permalinks added. I wonder if I can get myself named as a DOI or LSID authority, then I can immortalise my thoughts forever into the future.


It's all go here

In a fit of paranoia, I have decided to add a disclaimer to the bottom of all my web pages, including this one. This is probably unnecessary and legally pointless, but no one can blame me for not trying. For my next trick, I was thinking of fiddling with my stylesheets; quite a few dim-witted friends of mine have asked me whether I was colour blind, not aware that this the clash of colours is, in fact, a deeply satirical comment on society, the role of education and the monarchy in the 21st century. Suggestions for other possibilities in the colour palette are accepted.



I notice that the CBI are suggesting that the government should provide £1000 bursaries for students starting science programmes. Don't get me wrong, I think that this would be a good thing, but I can't help but wonder: would it not make more sense to just pay them more? After all, a bursary is a course, and salary is for life.


Bean Salad

The inspiration for tonights meal was by from my brother, who did me something like this a while back. A bean salad, with bread essentially.

Very simple: tin of mixed beans which I have had for quite a while — I think fresh would have been better; some fresh garlic, lightly chopped; olive oil; pepper; balsamic vinegar and lime juice. Served with an undressed green salad (with addition carrot and and parsnip), eaten with one of those boil-in-the-bag batton loafs.

Very simple, very nice. Back for more.


Facebook N^2 problems

The CARMEN project came to a grinding halt this afternoon. We decided to try facebook as a social networking site for the project. It turns out that everyone has to register everyone else as a friend; nice though it is to think that you have lots of friends, Facebook actually requires n squared number of clicks. Poor old Frank, being a young whippersnapper with lots of friends on Facebook, saw his laptop turn into the machine that goes ping as all his mates added him and sent him zombie requests; how does anyone get any work done in these days of social networking.


Comments in place

I've put comments onto the blog now. I've done this using HaloScan which is a javascript based system; I can insert comments without modifying the source of the blog. I'm a little nervous about this; I'd rather have comments under my control, but this seems the easiest way for the moment. It basically seems to work, although I had hoped that the comments would be injected back into the main page; something to work on.

Permalinks come tomorrow. With the comments, I have all the machinary in place that I need for this.


Eldon Square

They are currently knocking down one of the car parks associated with Eldon Square.

My question is, why stop with the car park?


In Edinburgh for CoKE meeting

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.


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


Harry Potter

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.


Last day in Vienna

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.


Viennese Cuisine

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.


Vienna Sights

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.


ISMB finishing

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.


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.


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.


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.


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.


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.


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.


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.


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


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.


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.


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.


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


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


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


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.


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 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.


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.


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.


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 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.


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 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.


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 claims to have no interviews) with an old monk. He was a deeply serene individual. However, he claimed not to be scared of death as he would be closer to God and that, moreover, there seemed no purpose to living for those without God. It's just a hop, skip and a jump from here to think that if death brings you closer to God getting there faster is a good thing, and that if people without God have no purpose in life, then they might as well not be alive. Even within this most gentle part of Christianity, we can see the ghost of the crusades.


Lightweight Repositories

Well, my rant of a few days ago did give rise to a useful discovery which is Nature Proceedings. Lodge your PDF, get back a DOI. Nature are doing great guns on this at the moment, although I think it's a pity that we tie ourselves to the mast of a publishing house.

I will definately consider going this route for next year. Maybe would just ask all authors to just submit here, and send us a DOI.


Cafe de Vie

Went to the Cafe de Vie for lunch today. It's quite nice inside, although would be better without the music. The menu was okay, rather than inspired: it's basically posh sarnies, italian style, served by the French. The food looked okay on the counter.

Their service was interesting: the heated food (toasted sandwiches, sorry panini's) was very slow to come. When it did come, the waitress described it in French, and seemed genuinely surprised to be answered in English. Everyone else got their food, but mine never appeared. I went and asked; they had forgotten.

So, no idea at all what the food is like, but I can say that it did offer a genuine and authentic French experience.


Institutional and Subject Archives

I've been looking at options for storing papers from bio-ontologies. All I want is a place to lodge PDFs, with some standardised Dublic Core metadata, and get a DOI out. It's turning out to be surprisingly hard.

In the process, I have found that JISC has been funding a repositories programme. If you look at their architecture you see a depressing thing. They have actually got terrible idea that "institutional" and "subject" repositories should be built into their architecture. The point is that institution and subject should be just a part of the data model that are used to store papers; by making it explicit in the architecture, it becomes fixed, unchangable.

Why do I care? Well, first as a cross-disciplinary scientist, I am also scared of anything organised by subject — I always tend to fall between the cracks. As for institution, why would anyone thing that 100 year old, bureaucratic, administrative orgaisation of the employers of the paper authors are a good basis for organising modern science?

The best I could find is Depot, but this describes itself as a stop-gap till the authors get a proper institutional repository. Also no one is using it. It's got one biological paper, and that's under the subject heading of "Biology not elsewhere classified" — a sin against good classification if ever I saw one.

The subject classification comes from JACS. From their documentation,

C190 Biology not elsewhere classified Miscellaneous grouping which do not fit into the other Biology categories. To be used sparingly.

Entertainingly, this has a subclass (!!)

C191 Biometry Concerned with the quantitative techniques and measurement in the biological Sciences.

Which as well as being a contradiction, is a definition that is wrong.

Perhaps I should just give up and go home.


Paco Pena

I first went to see Paco Pena years ago at the Corn Exchange in Cambridge. I've managed to miss him ever since, mostly because there was something else on at the same time; this time it was Bo Diddley who was playing. He has sadly had a stroke and the concert was called off. It's an ill wind, as it mean that I got to see Paco instead.

The last time I saw him solo. Now he has three guitarists, two vocalists, a percussionist and three dancers. Flamenco is arrogant, brash and melodramatic; Paco Pena's show lived up to this. The music was wonderful though, and the dance astounding.

I have to be honest and say that I prefer the music: the stage lights were quite bright (I was sitting at the edge of the stage, directly in the path of from lights from the other side). After a while, my eyes got sore. And I missed the intricate and flamboyant playing of 15 years ago; we only got a single solo piece.

Still, this is to be a curmudgeon. The night was wonderful; the music compelling and exciting; the adrenalin made my knees go weak. I hope that it's not another 15 years before I get to see him again.



My pension document arrived today. On the 28/02 I have been in paying a pension for 7 years and 43 days. That's a lot of cash, especially given the chances that it's worth more than a packet of smarties when I am 70 are small.


Green Festival

Went to the Green Festival in Leazes Park at the weekend. The weather was great — cloudy on day two, but still nice and warm.

I like the Green Festival. It's easy to be cynical — 100s of Geordies saving the environment by swilling beer out of plastic glasses. But it's got a great feeling to it, relaxed and comfortable. And this year, the music was better than last year.

Amusingly, at one point a drunk guy decided to go swimming in the boating lake. Got an enormous crowd. Slightly depressing for the musicians; you spend years learning to play, getting songs and rehearsing and then get upstaged by someone drinking too much beer and cavorting in algae ridden lake.


Google Calendar Fixed Undisaster

As described previously, Google Calendars was broken for me. But, magically and randomly, it appears to have fixed itself today. Thanks heavens for that.


Simple Kid and Groove Armada

Bit late to be writing this, as both gigs where a while back.

I've never heard to Simple Kid but Dan suggested the gig, bought the tickets and then found that he couldn't go. Which was a pity because it was a great gig. Simple Kid looks like a hippie Bjorn Borg. He writes catch songs with driving drums underneath; he's actually a pretty good guitarist as well, playing some fine solos. The obvious comparison is Beck, but you need to throw in a slice of Glen Tilbrook and Jimmy Page as well. His show is solo, with a laptop playing backing tracks, images, and sometimes lyrics. Strange set up, but it worked well. He has a great sense of humour as well, which really made the night.

Groove Armada on the other hand, I've written about before. They were great live, excellent music, funky light show. If I were to make on criticism, it was that the didn't turn it into much of a live experience. Even one "hello, Newcastle, let me hear you!" would have been good.

The crowd was a bit brusque. to be honest, and it was full sardine time inside the venue. It's good for music to be a shared experience, but this was a little too much. So a good gig, but sort of a once a year experience.



Decided to register for facebook today to see what it's all about. Did not get off to a good start as it would not accept my name as "legitimate". Ended up registering as "John Smith".

Entertaining. Wake up people. Lots of people have lots of different names. Blacklisting on words does not make sense.


Enormous rant

I've just been engaged in an enormous rant about the Access Grid. This is video conferencing software that I've been using for over 5 years now. It's dreadful. I live for the day that we can dump it, especially now that skype and teamspeak have outdated it. We shall see...


Bad start to the day

My coffee machine is broken. I have alternative facilities somewhere, but I can't seem to find them. What am I to do?

I am to buy a new one, that is what I am to do.


Google Calendar broken disaster

Google calendar — or rather google mail — seems to have broken for me. Instead of giving me an "add to calendar" button when an event comes in, it blithely tells me "sign up for calendar". Well, I already am! And events gets shown randomly translated into a US timezone.

This is really, really bad! I've come to rely on an electronic calendar, and without it I am in real trouble.


James Burton

Last night was James Burton at the Cluny. It was one of those "last chance to see" experiences, as he's getting on a bit now. So I was not sure what to expect.

The support band were dreadful — acoustic, electric and double bass. The bass player slapped his fingerboard a lot, with the resultant dull thud being all you could hear. The other two were more tuneful, but didn't appear to listen to each other. Rock-and-roll has to be in time or it's nothing but awful.

The second band were much better. Tight, together and with a sense of performance. By this stage, though, I was getting a bit nervous. Where was James Burton? Well, eventually he came on. Not that the flames on the telecaster work that well now to be honest, but James himself is still a strong player. Flash when he needs to be, tasteful when not. Above all, he is a side-man — he is not there to attact attention, but to support the song, to reinforce the rest of the band and to entertain the audience, which he did all evening. The support should take notice.

Of course, I paid a price. I got home at 11:30 — I've been up since 5 and am in an airport. I feel terrible. I guess it all boils down to what Gerry said — most of the audience didn't have to get up to go to work the next day, having retired some years before.


Bins and Stones

On my way home today, I noticed that one of my local metro stations has sprouted rubbish bins on the main platform. This is a bit strange, as I haven't seen them for a long time — I wonder if there is any realtion to the North Ireland power sharing agreement. They seemed quite out of place — being just bag and hoop bins, although I noticed some proper Newcastle Council bins lying next to the track outside. A hopeful sign.

When I got home I decided to sharpen my knifes as they had all got blunt. I've been meaning to try this for years, but I pre-oiled them with olive oil — I never fancied having the synthetic lubricants that I use on my bike on my kitchen equipment. It worked rather well, and made the process rather pleasant smelling — it takes the metal shavings away from the stone afterwards. One thing I couldn't work out is that the oil soaked into the stone. I guess Silcon Carbide is permeable to oil in a way that it is not to water, but to see a heavy stone soaking up a liquid seemed impossible.

I looked up wikipedia for an explanation; one was forthcoming, but I did learn that pure SiC is transparent; it only looks black because of Iron impurities. Now how useless is it to know that?



Noticed today that azureus, also called zudeo has now become Vuze. I noticed this because a new version has appeared. After an hour or so, I worked out how to switch of the silly interface.

One of the ironies of the situation is that the BBC content is currently not available in the UK, just in the US. Strange. I could have sworn that I paid for this stuff first time around.


Rebellion or what?

I was a little bit saddened to find the kerfuffle over an encryption key for HD-DVD being reported as a 21st Century Rebellion.

Don't get me wrong, here, I find the idea that industry should have the right to control how we watch films distasteful; I think it will limit what we can do with the digital content that we choose to buy; I think that it will result in horrible user interfaces, with limited choices; I think it will result in far more control being placed in the hands of a few people than is healthy.

But in the past, rebellion meant slaves struggling for the freedom, workers struggling for the profit of their own work, minorities struggling for civil liberties. It's a bit sad when this it becomes posting a number on a website like Lets face it, if anyone gets sued, it will be the admins of digg, not the people posting. This is hardly standing up to be counted, now is it?

At least some of my chums had the guts to put it up on their own websites. Still not exactly Tom Paine but at least it's a start.


BFO and Connotea

Well, I am not sure that my brain wave on conductance worked quite as well as I had hoped. Can't win them all.

I've been playing with Connotea which is an online reference manager, with added social networking. It's quite cute actually. The basic idea is sound enough, the interface reasonable. It allows commenting and you can look at other peoples stuff also. But it would be a hell of a lot better if it worked all the time. It seems to fail on a lot of DOIs, doesn't seem to work on pubmed as it is advertised to do, and can't work at all with sites that it doesn't know — you would have thought that some heuristics would do the trick for most pages. After all, it works for Google scholar.



Spent a large part of this week arguing about conductance and how to model it ontologically, with Pierre Grenon one of the authors of BFO. The basic scenario is a membrane — is conductance a property of the ions travelling through it or the membrane?

I won't repeat the argument here, but I had a blinding flash of light last night and realised what the solution was, which I shall post tommorrow. I even know how I would represent the solution in an OWL ontology. How this maps to BFO, I have no idea, and I'll be interested to find out how it works.

It's been an interesting discussion; I am still rather sceptical about BFO, largely on the grounds of its supposed "realism". I don't understand this. Claiming to be representing reality appears to me to be rather arrogant and, essentially, faith based. Worse, I can't see clear criteria for determining whether something is real or not. Is a the notion of a dimension real or not? Or does it depend on whether they are representing space and time or something else? I can't see it. More over, if you insist of representing "universals" rather than concepts, I don't think that you are can represent multiple (potentially contradictory) descriptions of the same observations; in short, you deny the possibility of an extra layer of abstraction, which I think that you need.

Having said all of this, I've enjoyed the discusson with Pierre. It's been hard at times, and we've worked through the example slowly. He's seems to be a nice chap. This seems like a good thing to me. I'd like to understand the realist position better than I do, and it's nice to find someone who I can talk with discursively, even when I am rather dubious about their technical position.



Spent today fiddling around with Je-S. This is the web portal that a number of the research councils use to submit grants.

It's a delightfully baroque and obscure piece of software. They appear to have worked very hard at the usability aspects — it would have been hard to make a system this unusable by random chance.

The system stores a grant in a two deep hierarchy with a small amount of information at the bottom of each. The end result of this is that you have to click down, then up, then down, then up to find out anything at all about exactly what is in the grant.

They also have this fabulous system for logins. Basically, if you login, and then don't do anything for 20 minutes, Je-S will automatically log you out. This would be minorly irritated. The designers clear thought that this wasn't good enough, so as well as loging out, it locks the entire system for another 20 minutes preventing you from loging back in. When it does this it tells you:

"This account is already in use. Please ensure other browser sessions are properly logged out before attempting to log in."

It clearly knows that you are not logged in because it logged you out, but obviously telling what you have actually done would be too much like hard work.

The whole idea of the portal is really good; we used to have to submit kilos of paperwork by post in quadruplicate. It's amazing that some software engineers could take such a perfectly good idea and completely strangle it. They appear to have managed to make a user interface which is SO bad, that you hunger for the days of word docs and print-outs.


More Hamish

Just watched the last of the second season of Hamish Macbeth. I won't say what happens as I know Dan reads these pages sometimes; he loved the previous DVD which I introduced him to, and I can't spoil the surprise. Two episodes in a row. And like before, they had me in tears. Fantastic stuff.

It's midnight now, and I'm away for easter. I promised to not take a computer with me. I'm left with no choice. So, I better stop typing and watch the last episode of the season. The thumbnail has Lachie jr, dressing up in drag, so I guess it's a funny one.


Swan Hotel

Staying in the Swan Hotel last night in Harrogate. Temperature was a bit hot but an open windows cooled it down okay. The rooms are really quite small — the bathroom is particularly strange. The loo is hidden at the far end, with a wall in the way which has means that to get to the loo I actually have to walk through the gap sideways. A bigger person might not actually fit.


British Neuroscience Meeting

Yeah, this isn't an April fool. It's Sunday, and I am working. Today is the kick-off meeting for the CARMEN project, and tomorrow we move into the British Neurosciences Association meeting. I've never been to a neurosciences meeting so I am looking forward to it. We've spent the last few days getting a demo working for it, which has been fairly stressful — as demos tend to be — but we got it working in the end.

One of the recurrent themes, that I've heard before within CARMEN, is that people are more than willing to give us their data; if so, it will run counter of many of my expectations. In general, getting anyone to provide data and sane metadata is a hard task; I really hope this works straight-forwardly within CARMEN, and that I am proved wrong.


Devon Sproule

Went to see the wonderously named Devon Sproule last night at the Cumberland Arms. The venue was wonderful; an old fashioned boozer, comfortable, with an open fire and an equally open view over the post-industrial view of the Tyne, nestled in the less than salubrious surroundings of the Byker Bridge: the pub predates the bridge, it seems.

The gig room is small, closed and deeply personal, painted in red and wood. My legs were cramped for the whole time, because if I stretched out I would have kicked the stage mic stand over. It suited Devon Sproule down to the ground. The gig was gentle, intense and personal. Her music is lyrical, her guitar fluent and her voice delicate; there's a slight tendancy toward being little girlish, but it wasn't overwhelming. In the second half, she was supported by bass, drums and later pedal steel, but Devon managed to cut through none-the-less. When the room got hot, the fire escape doors got opened; I listened to the music while watching the British buses and trains rolling past. I like to think that, perhaps, the music bleed out over onto the bridge, and caught a few people who wondered where it all came from.

One of the best gigs that I've been to for a long time, at a perfect venue. I'll be back there again, thats for sure.


I hate power supplies

Just got home. Tomorrow, I am going to Edinburgh, but I've left my laptop power supply at work. I'm not going to pick it up and get the train at 7:30.

Pretty pathetic really. Why do laptops all have different power requirements? I can see varying voltage requirements, but all the different shapes and sizes? At the end, this variety is not for any good reason, but for an economic imperative. Vendor lock-in, to the direct deteriment of the user.

Going to be interesting doing a workshop laptop-free for the first time in ages. I'm falling back to old technology — pen and paper.



Busy weekend! I watched Gattaca last night also. I have to say, that I was unimpressed. The story was contrived, unbelievable and with a cheesy "human nature conquers all" happy ending. The design and direction was quite interesting, lots of angles, single colour-washed shots, with 50s or 60s stylism everywhere, except that it's all been done before from Brazil onwards. The film has a big message hidden within it — hidden in the sense of crassly stamped over the entire enterprise, with a sense of moral self-importance rarely seen outside of Star Trek.

Music's good though.


Life is Beautiful

Finally finished Life is Beautiful last night, which I started last weekend, and have on rent from Amazon for nearly a month. Very strange film; how did anyone come up with a slapstick holocaust film? It was wonderfully acted, funny and adept. The story is compelling, sad and, of course, beautiful.

I found the second section rather disquieting. The concentration camp was basically clean, the inmates reasonably well-fed. Just occasionally, the gas chambers and slag heaps were thrown into your face. I didn't find it exploitative at all, though. So, perhaps, the disquiet comes from the subject matter. I guess, bringing humour to the holocaust allows the audience to think of it afresh.


Thea Gilmore and Erin McKeown

Saw Thea Gilmore and Erin McKeown in the Sage, hall 2 on Friday. We were sitting in the seats which seats behind the stage — strange, but I quite like it there, because you are very close and can hear the sound outside of the amps. Apparently these seats are renowned amoung performers, for giving the audience a good view of their backsides; it's not actually true, as the angle is too acute.

The evening was truely excellent. I've never seen Erin McKeown before, but she is well worth seeing. She's a much better guitarist than I had gathered from her recordings, and has a fine pair of lungs also.

Thea Gilmore, on the other hand, I have seen before. The last gig, I remember, was wonderfully well but together, with strong, lyrical songs. All this was still present but, I think, she has been practicing her voice, which was richer, warmer and stronger than I remember. She closed the gig with an acapella song, which I don't think she would have pulled off before.

The gig seemed to have sold out. It's nice to see talented people do well, but it's also has an unfortunate side: next time, she may well be in hall 1. All of the intimacy and warmth will be lost.



Having a wonderful time at the 2nd Ontogenesis meeting. I've just escaped from teaching for the year, and have managed to fill my diary for the next two weeks with research.

There's been a large amount of discussion about ontology building. The practical upshot of this is that the two most important tools are the phone and the plane. It's all about talking to people.

We need more and better tools for allowing collaboration on ontologies; we need easy to use interfaces which encourage people to make small contributions, while remaining formality. We need to make better use of the internet — skype has turned out to be a boon, but it's telecon capabilities are poor. Best of all, we need to be able to put our feet up, share a coffee, beer and scrap paper without being in one place.

I think my proudest moment was when I spent 5 minutes managing to make the point that sometimes people take a long time to actually say anything.


Wild Error messages

Was particularly pleased to get the following error today:

I would have been somewhat less pleased if it had happened the next time I rebooted but, fortunately, it all sorted itself out.


Mothers Day

My mother was very understanding about me forgetting Mothers day again. It's not true that I always forget, but it's not the first time. I even saw the scrum last night in the supermarket, with people buying flowers. This morning? Not a memory of it.


Silly Ideas

A first for me today. I have had an ongoing Silly Ideas wiki running for sometime, but someone finally tried one of them today, namely by Portable Music idea.

Perhaps this will spur me on, as I haven't written up a silly idea for ages.


The Falklands

I just listened to the archive hour on radio 4. It's an odd programme: sometimes it's dreadful ("in 1950 there was some obscure entertainer on the radio who was dull then and is worse now"); sometimes it's excellent.

Today it was about the Falklands invasion with recordings of the Island radio. The Falklands conflict was as enormous political event of my childhood, and I have many conflicting feelings about it. But the invasion itself involves a civilian population, with a few soldiers, at the end of military invasion they could not hope to stop. The archive hour described the events in a simple and straightforward manner, leaving the drama of the recordings to tell the story. The broadcaster showed extraordinary bravery, speaking to his children, then hoping for a return of the Islands to their peaceful state.



In the shop today, I noticed that they had some frozen soy beans. So, I thought I would give them a go. I've always been a fan of edamame that you get in Japanese food shops, so I decided to try and replicate it. Sort of. The beans were not in pods and I don't have a steamer.

In the end, I boiled them with some fresh garlic that I had, strained, the water of, tossed them with chilli olive oil and soy sauce (heat and salt), strained the excess and eat them. Nice actually. Needed a bit more than the 4 minutes simmer the packet said, so I ended up giving them a quick microwave.

Not bad, although not exactly refined. I need to work on this one.

The rest of the mean was dry, curried tofu and chickpeas, a spinach curry and rice. Done this many times before. I need to do it more often, not least as I appear to have 3 kilos of spinach in my freezer.


Everything Up

Took rather a lot of messing around, but I should have an "Everything" page now. The problem was that people kept saying I never posted anything. In reality, it's because the posts were split among four feeds. So, now, there are five!

As it happens, this is was a good thing. I use muse to generate these pages, but I've had to hack it a bit to split the files up — I want to maintain a single source file but then generate out a one per month chunk of HTML.

Muse is quite clever; it works out whether output files are out of date, but assumes that there is only a single file. I'd hacked the code so that it checked all the output files. This never worked well, so I've removed it. Things seem to work better now and there are less changes between the publish function supplied by muse, and the one I overload it with.

Perhaps, I should just take Dan's advice and use a content management system. But, this way I don't need databases and all that malarky.



Part of the infrastructure at Newcastle moved over to the Shibboleth provided by SDSS, at least as far I can tell from the login screen.

It's fabulous. The idea is to provide a federated login so that, at least as far as I can tell, login information is managed at a single point, and allows authorisation at multiple institutions. All of this sounds like a good thing, but they've actually managed to achieve the notable success of making logins harder than it was before.

In the past, I would go to a URL like, which is our coursework system, be presented with a login screen, which would login me into the system. Nowadays, I get take to a screen like this:

The purpose of this form is to let me tell the browser to go back to the system that I asked it to go in the first place. There I get another login screen which, to make our life easier, has been nobbled so that the browsers won't remember the logins. It also seems to be crashing a lot now, so that you have to refresh your browser to get it to work.

The help link, incidentally, at the bottom takes you to a page which tells you:

SDSS Development Federation

The SDSS Federation no longer accepts new applications to join the federation. Applications should instead be made to the UK Federation.

Help is not forthcoming.


Firefox irritations

When it first came out, session management was put forward as a feature, but I am starting to think that the inability to turn the damn thing off is actually a bug.

If you turn the OS off, with firefox still running, then it thinks there has been a crash, and offers to open all your pages again which I never want — if I have turned the machine off I am unlikely to remember which pages I had open. If there has been a crash, then having Firefox open all the pages again, one of which made it crash last time, seems like insanity.


Foundational Ontology

Prompted by Matt Pocock, I've just had a look at the basic foundational ontology. I have to admit to have been left feeling very confused. SpatialRegion have to be either a Zero, One, Two or ThreeDimensionalRegion which seems to preclude other dimensions. They are suggested to be immobile, but I can't see that this has any meaning. Also, SpatiotemporalRegion is a sibling of TemporalRegion, but not SpatialRegion (they share a common grandparent) and all three are disjoint from each other.

More reading is required, I guess. Unforunately, the documentation seems a bit long. The BFO in a nutshell document is 37 pages in total.


More pandora obsessive behaviour

Jolie Holland's latest recording has been hitting pandora recently. When she was in the Be Good Tanyas, I used to find her strange, wandering phrasing curious, but on Springtime Can Kill You, it's compulsive listening. She seems to wander through her lyrics, producing music which is melancholic and lazy. Mexican Blue stands out for me; the lyric is elegant and personal, and melody simple, and the orchestration minimal. It's unclear what makes this song so compelling but it's there no the less.

It's turning my into an obsessive. I must have listened to it 20 times in the last two days — more if I include the times when I was working the chords out. Pandora is bad for your health.


Installing Acrobat

Acrobat is a highly irritating application. It always tryies to be smart-ass and does far too much. Today, just trying to download it failed. The adobe site insists on using a download manager, which was just crashing.

Eventually, I managed to get the metadata file that the download manger uses — embedded in this was a URL. 10 seconds later, download complete.

Adobe, sort your life out. I just want to read a document. How hard can that be?


Jess Klein and Chris Knight

This was the first time I have been to the Cluny. It's a good venue, being a converted warehouse. The main pub section is open, but warm in feel, although having so much brick around is a bit noisy. The food was good, although as I'd already eaten well at lunch it was overly large.

As I've said previously, I first heard of Jess Klein on pandora, and was lucky enough to see her tonight just a few weeks later. Dressed in black, set against the light, she seems small and vulnerable on stage; the effect accenutated by her guitar, a Gibson J200 I think, which is huge; the soundbox dwarfing it's owner. Her music, however, belies this image. Although, some of her songs are quiet and gentle, quite a most of them are belted out, her vocals strong and clear, the guitar strummed with fervour of a busker. Put on top of some melodic, and well-paced songs, it makes for a compelling performance. She's not the best lyricist in the world and, perhaps, overuses the power of her voice but, in general, she's well worth seeing.

Chris Knight, I have never heard of before. The introduction told us that he was from Slaughter, Kentucky. He gobsmacking accent confirmed this — I have a bizarre image of him swapping stories with a bunch of geordies afterward. Chris likes to sing about bad things. He got married at 16, and 18 and 21, his various wives gave birth in many bad situations, and he's killed a lot of men. Still, you could feel the anticipation in the audience; we waited patiently all night for it and eventually, we heard what we had all been waiting for and Chris called the audience "y'all".

Well, this might all come across a bit negative, but I enjoyed a lot of his performance, it just went on a bit longer and got a bit familiar.



I've been totally obsessed recently with Pandora; basically, they have defined a feature set for music, attributed this set to a library of music and there you have it: theme-based, personalised internet radio.

I've discovered some many new musicians this way. Ani DiFranco is playing at the moment (who I knew before). But Melisa Ferrick and Erin McKeown I'd never heard of before. Jess Klein, I am probably going to see at the Cluny this week.

At times, you think that talent is a rare thing, but, then, there are so many people in the world, there is a continual stream of excellent, surprising and exciting music and art being produced. The traditional media has limited us massively; we get to hear so little of what is available. It's not really a surprise that the various social networking sites have been such a success.


Keybinding For Cygwin

When I moved up to Newcastle and had Outlook inflicted on me for a while, I moved to using a trackball. I've found that they are much, much easier on the wrist for mouse-heavy applications. The experience has generally been good. However, logitech insist of supplying mouse drivers which attempt to be clever, and do the right thing all the time. One of these things, was to screw up cutting and pasting into a cygwin window. Finally, I have found the solution:

bind '"\C-y":paste-from-clipboard'

Emacs keybindings in cygwin: what more could you want?


Tofu and Noodles

Tried a new technique last night; basically, I just slow, shallow fried large lumbs of tofu. After a while, once they had sealed, I threw in some cayenne, garlic and, then, some Udon noodles with a bit of stock to let them cook.

Worked pretty well, as it happens. Took ages, as you'd expect from a bit lump of tofu, but required little effort.


Soothing an irritation

This morning I got up early and came in for a session on module design, as part of the PCAP course. I was irritated to find out that it actually wasn't on at all, and that I had completely wasted my time in coming in early (which, if I was being uncharitable, I might think would have been what happened anyway).

But all is not lost. I found the solution to a problem that has been bugging me for ages. Once upon a time, I managed to type my email address as, by mistake, into firefox. It's been offering me this as a completion for the last year. I have finally found the solution on a blog — select the option, press shift and delete, and it magically disappears.


Learning to Teach

Have spent the last three days doing a teaching and learning course. I wouldn't mind doing this course but, like most academics, I'm fairly overloaded and would be more interested in doing my own research, rather than listening to others talk about research that I am not that interested in. Still, there have been sections of the course that was quite interesting. I'm a bit distressed to find that I found the section of resource allocation — that is, how the finance system of the university system works, and where the cash goes — has been by far the most interesting section. What am I turning into?



One of the things that annoys my about politics is the tendancy to massively over-interpret information. The recent spat over the education of Ruth Kelly's son is an example. She's decided to send him to a private school, as it would appear to be more appropriate for him.

As far as I can see, the conclusions that you can draw from this, is that for one child, with one set of learning difficulties, in one area, one private school appears to be better than state provided options. Interpretation made in the press is that this means that any child, in any area, with any learning difficulty would be better off in private education.

It would be a shock, indeed, if you could find no child, anywhere, who was not going to better off in a private school.


To the Manor Born

Today, I am at a research away-day at Slaley Hall. This is a De Vere hotel, which I am sure is the name of Peter Bowles' character. The whole place has a wildly expensive feel to it. Internet access is 15 quid for a 24 hour period, which is probably about a markup up of about four orders of magnitude.

When I was younger, I thought that the difference between an expensive hotel and a cheap one would be the basic quality of the experience; better beds, nicer food and so on. It's not really true though. Expensive hotels have exactly the same problems as cheap ones: soft beds, bad food, light pollution from the corridor, noisy mini-bar and air con and, worst, people having sex upstairs. The difference is that the add-ons, that you don't use anyway, are better. The free biscuits are nicer, the grounds are better (Slaley Halls are very nice, but water-logged at the moment) and the naff art-work on the wall is a cut above.

Okay, so I'm grumpy, but the air-con kept me awake all night. Air-con. In Northumbria. In winter.


Christmas Offerings

Perhaps it's a bit daft of me, expecting too much, but I'd hoped for some quality entertainment over the Christmas break. I have to say, I was most disappointed by the general quality of the TV.

I was looking forward to the Ruby in the Smoke, which the BBC dramatised; I'm a great fan of the books. Somewhat inevitably, Sally Lockhart was played by Billy Piper, who appears to have become the BBC standard feisty hero. She was okay although, perhaps, a bit old (Sally is 14 in the book). Julie Walters was excellent as always. In general, the film I think lacked over the book. They cut out too many of the incidental details which provides the books it's richness. The sense of the Sally fighting against society was lost. One thing they left in, was the death of Mrs Holland. I always thought this was weak in the book — the lead baddie , randomly decides to kill herself, in an act of desperation. Why didn't she kill Sally?

Speaking of Billy Piper, the Christmas special of Dr Who was excellent. Sharp action, witty dialogue and an entertaining baddie.

As for films, there was nothing new. The best were Unforgiven, and Pirates of the Carribean (terrible ending, pointless special effects but entirely sold by Johny Depp). Ah, well, maybe the new year will bring something better.



Been trying out Zudeo. Basically, it's Azuerus with a nice front end. It doesn't take too much to get behind the front though: strange messages about NATs, UPnP devices and port numbers pop up with regularity. They need to think more if they really want to sell this to the mass market. The basic idea of a high quality version of YouTube is fine, but it takes too long at the moment for the download.


Christmas Spirit

On the metro this morning (my bike is in dry-dock), there was a women with two young kids (2 years old say), who was encouraging them to sing Jingle Bells and other such seasonal favourites.

Actually, encouraging them! I mean, did she not know, that everyone else listening to an out of tune, kiddy-drivvel version of Jungle Bells just wanted both of the cute small kids to be quiet? Or die. Horribly.

Climbing the stairs to the way out, I was greeted with "Bing, Bing, Bong, The Metro would like to wish you all a Happy Christmas". What's the point of a recorded service announcement about this! Am I suposed to think that a piece of tape is showing sincerity? Canned, automated, templated Christmas greets are a scourge.

Merry Christmas and a Happy New Year.


Pandora's Box

Did my taxes this evening. Turns out not to be that hard as it happens, although I was ably assisted by Mike Aird — I mention him, because the last time I put him up a friend of his got in contact as a result. Tax forms in the UK are a right bugger, although easier than many places I believe. I've realised that doing the work was a mistake though; filling in the forms costs more than what you gain.

Spent the rest of the time waffling on about the power of the internet. I heard Erin McKeown's "Fast as I can" the other day, randomly, and was struck by the beautiful use of inverted word order, leaving the whole thing with a real spacy feal. I heard it at work, then forgot who did it, but 20 minutes of determined work with the internet got me the artist, a short hop to the lyrics, a few more got me an MP3 (sample, obviously, not the whole lot), and another minute to find that she's supporting Thea Gilmore at the Sage in a March.

The course I want to on Information Literacy last week, would suggest that I got this all wrong. Apparently, free text searches are bad, and I should really be using structured searching with boolean queries in a database. True 10 years ago, but now? Boolean searching was a bad user interface because we didn't know how to do it better. But 20 minutes to so much information about a song that I half heard a week before? Now, we do know how to do it better.


Annoyingly Visible

Just listening to Radio 4 and getting a bit annoyed. A few weeks ago, there was a daft story about invisibility cloaks.

Look, I am sure that it works really well, and potentially it's going to have major technological applications. But it only works with one wave length. In what sense is this invisibility? Have we really reached the stage, where scientific reporting is based purely on how many inappropriate cultural references we can throw in? I like Harry Potter, but this is really starting to put me off.


Crash on the A1

I drove passed a crash on the A1 yesterday. One car was facing in the wrong direction along side the central reservation. It's pretty depressing really. Everyone was very measured about it, with all the traffic slowing down and moving passed in an organised way; this was before the police had got there. But no one stopped. Once one person has done it, we all follow along, without any though of even offering help to those in distress. It's a sad reflection on the isolation of modern life, sitting in steal boxes.

Still, the road afterwards was really clear for quite a few miles, so it's not all bad.


Casino Royale

A new James Bond has happened. Hard to have avoided this with vast amounts of plugging going on; the BBC News appeared to turn into the advertising wing of the Bond machine for a week.

Went to see the film in the Vue cinema in Worcester. Fairly horrible place, lets be frank. When you come in through the door, you are assaulted by a wave of fat smells from the popcorn and ice cream. The foyer is actually quite tatty now, despite the fact that it's relatively new.

An initial feeling of relief, sitting comfortably in the cinema seats (the Vue has got this bit right), is soon blown away by the assault of the 30 minute pre-film advertising and "Copyright is theft" propaganda. Finally, the film starts. Sadly the advertising doesn't. James Bond driving his Form, using his Vaio, phoning on his Sony Ericsson. It's got to the point where it totally disrupts the flow. Combining it with the new, darker, more serious Bond makes it even worse — the new film has a sense of self-importance about it, which is totally punctured by the adverts.

It's not all bad, though. John Cleese is no longer in it, which is one hell of a relief.


Schizophrenia as a use case

At a workshop in NESC, looking at data integration in the Neurosciences.

Very interesting talk from Maryann Martone. She showed a slightly depressing slide describing the aims of the various eScience projects which is basically interchangable between all projects — data heterogeneity, distribution, autonomy. Like other medical research projects that I have heard off, they spent nearly three years getting the data through the various ethical approval committees before they could even think about hosting the data. The requirement for anonymity is important, of course, but the cost is enormous. It's a pity that this effort can't be shared for different projects.

Neurobase presented an interesting architecture which looks very like ComparaGRID — they have a set of wrappers mapping into a common relational datamode; essentially ComparGRID does the same thing but with an OWL based model.


Fat Men Dancing, Goodbye Lenin

What a weekend of culture! Simon and Rina came up from Friday, with the plan of going to see something called "Cairo Nights" or the Farha Tour (I was quite sure of the relationship between the two names). Basically, an evening of belly dancing. Rina's idea and I'm game for anything.

There were some delays on the way (Simon and Rina got stuck on the road, and I walked round in circles for a bit, as I'd not been to Northumbria Students Union before), so we got there a bit late. Rather disappointingly, instead of belly dancing when we arrived, there was a fat guy with a belt-line over his belly button and finger cymbals on stage; clearly, Newcastle is the place for middle-aged, post-op, transexual belly-dancers, I thought. The rest of the evening was pretty good, though. Nothing I haven't seen before — we did get belly dancing later on, and men-in-skirts rotating very quickly, and the bloke in a two men wrestling costume. And the fat bloke with fingers cymbals again. But it was actually a really good night. Most of the seats had long gone, so we just stayed at the bar cause there was lots of floor space there (like anyone is going to believe this), watching and dancing to the music. Highly recommended.

Saturday, we went to the Baltic which, I admit, is becoming a bit of a traditional thing when people come up to visit. I've seen this exhibition before: some of it very strong — the John Lennon tribute in the stairwell; some of it less so — the cartoon of the guy having sex with a dog (or sheep, there was some disaggrement on this topic).

I've been to that particular exhibit before. In general, I go to the Baltic often enough to see most of the exhibits, but not often enough to see things twice. I actually enjoyed seeing things twice.

Finally, this afternoon, I went for a bike ride and was feeling a bit pooped afterwards, so I watched Goodbye Lenin, which I've had for a while but not watched. Marvellous film. Very funny, poigniant, and set against German reunification. Humour, sadness and history — well, I was always going to be a sucker for this film, but it was put together very neatly, nicely directed and with lots of internal references which reward the audience for its attention. Always useful when you are tired after a bike ride.

There were two strange things about the film though. Firstly, I have a clear memory of Barry Norman reviewing it on the Film programme — but I can't have because it came out in 2003 well after he left. Was it another similar film I wonder. The music drove me mad as well, as I recognised it, but didn't know where from. Actually, it was the same composer as Amelie, and it's very similar. It worked well, but the sense of recognition was a bit distracting.


Spicy Tofu in Pitta

Did a Spicy Tofu in Pitta as Simon and Rina were coming up. I thought they might be late, and we'd be in a hurry (they were, we were), so I wanted something easy to eat of the move.

This is incredible simple. I cut the tofu into blocks about 1cm x 1cm x 2cm. This goes into a frying pan with some rice vinegar, soy, and chilli sauce. This is all fried in, on a low heat for, well as long as you can be bothered to wait. Within reason, the longer the better, but an hour is a reasonable time. This is then served in pitta with salad. I added some felalal as wel, as I had it in the freezer.

We only had time for a quick bite each. However, we left the gig at 11 and the curse of Newcastle hit us, with all the food places closed and we scoffed the rest when we got back.



Been watching season two of teachers. Entertaining, funny, slightly bizarre and with lots of jokes about sex. Hardly a surprise it was such a success, although I never even heard about it at the time it came out.

Not sure watching a programme about a bunch of malcontent, alcholic obsessives worried about the pointlessness of their own lifes was such a great idea though, not at the weekend anyway.


Calendar move

For the life of me, I can't get google calendar to use the correct reply-to address when sending calendar events. This is a pain. Once you let an alternative email out there, people will start using it whether you want them to or not.

Nothing ever works exactly as planned.


Calendar move

Well, the calendar move seems to have gone okay. I have a slightly baroque mechanism set up. Pulling down the ical files from google every night should give me offline access, in a read-only way using sunbird. I've then got an export caledar in sunbird which, by hook or crook, will eventually work it's way back to my website, from where google can pick it up. Then I can copy it to my main calendar and, finally, delete it when it works it way back to sunbird. I was going to give Calgoo a go, but I didn't like the look of their license.



I've been using Planner mode for the last few months, to keep track of appointments. I like it because it integrates well with Emacs, which is my main environment. But I've decided it just doesn't cut the mustard. It lacks two main things. Firstly, it can't do ICAL based mail negotiation of meetings. Secondly, it lacks a nice overviewer. I developed something which addresses the latter, but it's not enough. So I keep on missing early meetings, because I didn't see them coming up the day before.

In the end, I've decided to go for Google calendar. It generally integrates nicely with mail, although I'll have to check my gmail account periodically, which is a pain as I don't use it for anything else. The AJAX interface of the calendar is quite nice; I don't need to use it as rapidly as email, so that it's a bit clunky is not a huge problem. Pity that right clicks don't work.

Moving current events is going to be a pain, though. I think I shall keep planner, though, as a task manager. It's pretty good at that.



Well, I was a little bit worried about my talk, as the last time I tried it, it wasn't that good. But in the end, it went reasonably well, which was nice.

The Ontogenesis meeting was a good meeting — and only partly because I was enjoying doing research so much. There was lots of discussion on the softer aspects of ontology building. What metadata do we store about ontologies, how do we get information about of domain scientists and so on.

One slightly embarrasing thing happened — Andy Gibson refered to my talk during his, and then asked me a question about it. But I hadn't been listening, having written email most of the way through his talk. I have a good excuse: first, I'd trieda to rearrange the timetable and that had gone horribly wrong, as none of the students heard about it in time; and second I'd arranged for Keith to cover my practical session, but he ran over a dog and his bike and knocked himself about a bit. Even when I get let out for a bit, it seems teaching still has a hold on my attention.


Pasta and Friends

Last weekend, I went to Tesco's. Unusual for me, as it's some way off, although the food range is better than the local Asda, which is enourmous, but full of rubbish.

Supermarket shopping on saturday is strangely relaxing — the environment and general experience is so horrible that they only way I can cope is to let my brain switch off as much as possible and wander around in a meditative daze.

I spent 15 minutes trying to find soap — I'd assumed it was with detergent, but actually it was next to the dental floss. I also noticed that the pasta isle has been renamed to "Italian Meal Solutions". Very strange.

This weekend, one of my oldest (or should I say longest) friends, Phil, came up. In the end, we watched some vids and drank some beer. Actually, I watched the vids and Phil dozed off. I wonder how a man who is clearly so desparately in need of sleep is going to cope; he's going to become a father in a few weeks time.



I'm being let out of teaching for a few days to go to a meeting entitled "Ontogenesis", which is about ontology building as far as I can see.

I'm greatly looking forward to it, although being stuffed up in buffet car of an overpacked, overheated London train is not ideal. I'm going to talk about what appear to be the differences between neuroscience and biology in terms of ontology building — I'm basing the talk on ignorance and supposition as I hadn't been doing this for long enough to know better.

I trialled the talk on Friday. It wasn't very good. I should be working on it now, but the train is too horrible to concentrate on anything serious.


Motorcycle Diaries

The motorcycles diaries is the film of Ernesto Che Guevara's travels through South America. The story moves from it humerous and engaging beginning to its poigniant and moving finale. The film is wonderfully acted, beautifully scored and delicatly directed; it's filmed against astounding geography and a historical background more stunning still.

I've spent too long recently re-reading, re-watching. Who could wish for better than the Motorcycle Diaries to break this habit.


Dying for TV

Ironic, really, that two TV presenters should have been seriously injured or killed while filming, namely Steve Irwin and Richard Hammond; one killed by a stringray, the other by driving too fast.

The coverage of both has been rather irritating. The media has got increasingly solipsistic these days and likes talking about themselves. Personally, I didn't like either of them as programme makers, both pushing style over substance, both somewhat puerile.

Despite their similarities, however, there are differences. Steve Irwin made his programmes to highlight the animals he appeared to love in face of the risks to their existence, the loss of which would make the world immeasurably poorer. Richard Hammond appears on a programme about driving fast.


All Hands 2

Finally got back from All Hands. Could have done without the meeting really, as it's left me very tight for the beginning of term and a BBSRC grant deadline. Was a good meeting though. There was an interesting talk on a ontology of units of measurement — perhaps not exciting but everyone needs it. Peter Buneman gave a talk on why annotation is hard. His conclusion — that you need a reliable identifier system — seems fair, although problematic; reliable identifers have been discussed before, but they require coordination and probably centralisation. While I don't hold entirely with the "404 is a feature not a bug" argument, it is true that requiring this form of centralisation brings with it many disadvantages.

Ah, term start; bang goes any chance of sciece happening for the next few weeks.


All Hands

At All Hands Meeting in Nottingham. It's changed over the years from a very poor conference when no one had anyhthing to talk about to something more reasonable. Already had a couple of interesting discussions, one of which might help with getting a statistical ontology together for CARMEN.

The talks have been okay, although of widely different quality from the interesting to the inconsequential. One of the big changes this year is that people are spending much more time talking about their science rather than the technology which was used to achieve this. A very good thing, to my mind. It's important that this work be kepts grounded and if projects can't get someone to talk about the science then I think that there are problems. Also, you get to hear about some new areas science (crystallography at the moment) which has to be up from 15 talks in a row on "what I did with globus, web services, other buzz word".


French blogs

I was listening to a programme of blogging on Radio 4 a few days back. This weekend I had a look at one of the those featured, which was Petite Anglais. I wondered what it was that made it such a well-read blog. The answer is simple — the writing is excellent. It's witty, discoursive and makes you rethink its relatively mundane content. It also moves between strange and the deeply personal, and is moving because of it. In the end, though, it was probably this aspect which lead to the author getting the sack. The content does not actually justify her getting the sack. I suspect her employers were more worried about what it might say in the future, than what it actually does. I don't really understand this; I'm a fairly open person; I'll tell anybody anything that they choose to ask. My life is dull enough, that nothing that I answer is likely to be novel to anyone; they've probably done, thought the same things that I have.

The blog is slightly depressing as well, at least for me. I write for my job. Perhaps it's the formal nature of it that has robbed me of the ability to write quickly, lightly and with a human touch; more likely, I just never had the talent.


Reading Trash Fantasy

Read one of the Thraxas novels at the weekend. I'll say up front that they are good novels — funny, well-plotted, slightly bizarre — but they are not as good as Martin Millar's main novels which he seems to have stopped writing. A great pity.

Why was I reading this though? I've read them before, so there is nothing new to gain. I think that there are two reasons. Firstly, I seem some of Thraxas in myself. He's surrounded my amazing happenings, but can only rarely see it. My job is a bit like this. Looking back on the research I have done, and the changes that have happened in my life time is stunning. Like everything, in collapses into mundanity while you are actually doing it. The second reason is that I was fairly tired and hadn't slept well. Under such circumstances, you need something tight enough to interest you, but light enough to not demand too much thought.

It's a pity really. A few years ago (well, six or seven years ago), I went on a holiday on a boat. I was miles away from anywhere and trapped with no where to go. So I read a history book (E.P.Thomspon's, the Making of the English Working Class). I got 2/3's of the way through it, and have never finished it off. For such things you need a clear mind. Perhaps, I should go on another holiday, miles from nowhere.


Free as in Rubbish

Read a very bad article on the BBC website about free security software. Very bad because it suggests that people using free security software, may be using software which doesn't do the job, failing to stop many attacks or even importing trojans.

All, of course, entirely true, but providing the entirely false impression that software you paid for is going to do any better. Security software is like insurance — you don't know if it's any good, until you get in trouble. Actually, it's even worse with than insurance; when you crash your car, they might actually pay up. With security software, by the time you find that it's rubbish your machine has been trashed. However are you to purchase wisely, when you have no ability to judge, and where all the "experts" have a stake — they guy slagging off free products works for McAfee.


Unseasonal happenings

While looking for housing last weekend, I decided to take my bike. It's slower, but you can see far more from a bike than you can see from in car. It also reminded me of how much I like to be on a bike: watching the tarmac move underneath your wheels; wind in your face. Strange time of the year to get the bug for cycling again, but I was blessed with beautiful weather.


Heavy Traffic

Been having an interesting discussion on the relative merits of mailing lists as opposed to web forums. Personally, I hate having to read things in web forums, because I am always find the interface terrible, particularly for writing notes as you are largely limited to a rubbish text box. Part of the reason why I hate web forums so much, though, is because I am a Gnus user; it was originally a usenet, news group reader and it's user interface it designed for reading high traffic, where most of what you want you get, you don't want to read. When I was had to use Outlook earlier this academic year, I was in real troubles, because it's user interface could just not cope with large amounts of traffic — click, click, point, read, click, click, right click, mark, read — read by date or by thread, but not both.

However, during the discussion I realised that there was a display that Gnus doesn't do; it would be really nice if the summary display — a threaded, indented set of subject lines — could also display the first four of five lines of text underneath. Currently, subjects and contents are heavily mixed.



Went looking at areas where I might buy a house this weekend. I quite liked the look of Wide Open. The name sounds pretty odd, although my guess is that it dates back to the coal industry; presumably, there was an open cast pit there.

It looks quite nice to me. It's a little bit out of town; the bike ride will be significant in the morning, but this is not necessarily a bad thing. The houses are also a bit cheaper, so I can get something proportionality larger and with gardens. I like space, so this is not bad thing.

I need to find someone who lives there, though. The only person to offer advice so far said "oh my god, it's a tip". But she hasn't been there for 20 years.


PhD programmes

I've been trying to appoint someone onto an EPSRC Case studentship. The eligability rules are a nightmare. Apart from the fact that no one knows exactly what they are (I phoned up EPSRC and no one there knew!), they appear to be largely UK only. Other EU citizens can apply, but they need a three year residency in the UK. Stupid! The PhD is an international qualification. PhD students add immeasurably to the research environment. We should be glad that talented people want to come to the UK from abroad.

The core problem is, I think, that the PhD is considered to be an education, rather than a job. Thus, we have PhD students rather than researchers. This is only to the disadvantage of the students — they get treated poorly by the University system, it's harder to get loans or mortgages. Even the tax free status is a disadvantage — it saves the employer money, while the student comes out with a large gap in their stamps.

Ho hum.


Tofu in stock

I tried a new tofu dish last night. Very simple. I boiled the tofu in a frying pan with a stock made from some tamarind stock cubes, oxo veggie cubes and some garlic flakes, flavoured with cumin and MSG. I also added some rice vinegar which turned out to be a mistake as it was far too sour — in the end, it needed sugar to perk it up. Anyway, after boiling the tofu and reducing the stock somewhat on the hob, I toasted the top under the grill. Then, finally, returned it to the hob, added a little water to dilute the stock again, and sprinkled on raw garlic and onion. Left this for a few minutes till the onion was soft, and eat with ramen noodles.

Worked quite well, in general. As is my usual practice, I'll probably do the same dish again tonight, while it's still fresh in my mind.


Tabs online

One of my favourite websites, the Online Guitar Tab Archive, has been taken down again by foolish action by some lawyers. This has happened befor — in fact, OLGA itself only came about as a result of legal action. It's sad though, that some individuals are so threatened by others helping each other freely. I don't necessarily blame the copyright holders, who are just trying to make a living. But you have to wonder about a system which requires people to fight in such a ludicrious manner.

The IPR laws are getting increasingly insane. They continually block new ways of using technology. I am starting to think that IPR and communication are necessarily conflicted. I wonder which will break first.


Episodic happenings

People tend to look down on TV serials as compared to films; I think it's the notion that good art must be weighty and large. There are occasions, however, when you see a serial that really is astonishing. I've been lucky recently to see three of these. Some night, I shall watch all fo these in a row. To confirm the prevaling opinion that all scientists are trekies, the first one was "Sarek" from Star Trek—The Next Generation. The high point is that it allows Patrick Stewart to be terribly actorish on stage. It also features a bar fight and Wesley Crusher getting slapped my his mother; he could have done with more of this.

The second was a Hamish Macbeth episode that mentioned earlier, called "Wee Jocks Lament". It has everything that makes the series great — humour, sadness thrown together in a bizarre way.

Finally, and new to me, I saw "Aurora Borealis", which was the last episode of the first season of Northern Exposure. I've not seen this one before — I don't know when I started watching the programme. It's a masterpiece though. Three subplots tied together deftly and one of the most strange dream sequences of all time. Highly recommended.


On the tiles

Went out with two old friends from back when I did my degree. It doesn't seem that long ago, but I guess that it is. Mike Aird lives in Newcastle, so I've seen him a number of times since I got here, but I probably haven't seen Mark Dixon for a decade or more. So, I was reasonably looking forward to an evening of slightly fatter, middle aged blokes reminiscing about old days; but both of them are thin as rakes. Never try and chase up your past, it might tell you rather more about your present than you want to know.

Was a good night, though. Mark seems to be doing well, has accidentally managed to become called Chris, and does something engineeringy.


North of Fortaleza

Just got back from two weeks in Brazil. I've never been to Brazil or, even, South America before. All in all, I had a great time. Fortaleza, in the state of Ceara, is a relatively small town, and is very much centred around the beach — I saw a lovely newspaper headline one day saying "Ceara looses 7m of beach a year". It's not a place to go to for cultural highlights; I like this about conference holidays, though: the holidays you end up with are not ones you would have chosen, so it can be a surprise when you enjoy yourself. We had plenty of time for lying on the beach (although not for too long due to the sun and heat), went swimming and eat food. The beach in town (Praira do Meireles) is indifferent. It's long, but a bit grotty. Still, it's very shallow, so would be good for the kids. Outside of that, we got to Praira do Futoro which is long, golden, with lots of beach pools that are warm and swimmable for the kids, while the actual sea has quite a heavy swell. Great fun but only for good swimmers. We also went to the beach park for the conference do — the park itself looked chessy, but as they only let us onto the beach and feed us free food and beer, no one minded this.

Food in Brazil is reputed to be poor for the veggie; actually, I didn't think that this was so. It was boring sometimes, but, in general, I eat okay. And even if the dinner was dull, it was often more than made up for by the fruit juices which were fabulous and in enourmous variety; only tempered by the odd Brazillian custom of watering them down (a little bit of water in some, like mango, makes sense, but just a little bit) and adding sugar. As well as all that, you can get "um coco por favour", for about 30p and sit in a barraca sipping coconut milk.

I really enjoyed it. I'd love to go back again, although the chances are that I never will.


Run, Lola, Run

Don't quite know why I ordered this DVD — I guess mostly because it's a bit of a cult classic and I wondered why. On watching, it became fairly obvious. It's gots lots of wobbly, hand-held camera moves (sorry, this still make me travel sick, even if they are cool), loud and occasionally intrusive background music, some cartoon segments. The premise is an old one — what if things were slightly different, pick your own alternative ending.

As a film, it's not bad; it's quite watchable, even exciting at points, but in the end, I felt that I was watching a music video rather than a film. It has become a modern, cult classic — I doubt that it will become just a classic.


ISMB 2006

Pretty much as expected, ISMB was small this year as it was sited in Brazil; while those of us who got there really enjoyed the place, I think it put many people off. The small size of the conference made it very friendly and easy to find people, which was good. The centre itself was excellent in most ways, with the only really problem being the air con, which was fairly noisy and somewhat overwhelmed the AV.

BioOntologies took a particularly heavy hit in terms on submissions — most people needed a main conference publication to justify the travel. It was lucky that we had merged with BioLink for the year, or we would had to have cancelled the day. Hopefully next year will be better, as this is our 10th anniversary meeting — a long time for a SIG to be going.

The main conference was quite good; it's noticable that the days of the microarray normalisation and sequence searching talks are largely over; thank god for small mercies. The ontologies section was quite interesting as two of the three papers were heavily biological in content — Katy Wolstencrofts paper was excellent (okay, I am an author which makes my biased), while Larisa Soldatova gave a great talk on their experimental ontology, EXPO, written for the robot scientist, the videos of which were entertaining. The last paper, on a ontology of function was more theoretical, being about an upper or middle ontology. It seemed sensible at the time, but these things need to be tried out in reality — it's hard to make a critical judgement in the short term.

Next year is Vienna. It should be better attended, but I do wonder about ISMB. Bioinformatics has no reached a point where it is part of most biologists lifes. Those with a more theoretical bent are moving off in a systems biology route — this gives them lots of opportunity to argue and discuss which probably explains why, 3 years on, no one has a decent, clear and consistent definition of systems biology. Perhaps, Brazil will mark the ending of ISMB's day in the sun?


Going away

It's always pleasant to get home after a while away. I don't mind travelling, but after a while I feel alienated being surrounded by people speaking in strange gutteral accents, with words I don't understand. So, it's a relief to get back home to Newcastle.


Databasing the Brain II

Interesting day, so far. The talk on the "Cell Centred Database" was a bit of a highlight; looks like an extremely competant and capable system. They are using a very ontological driven system, and trying to incorporate annotation into the tools which are used to generate the data in the first place. Very sensible, although hits the problem that the ontological markup can be hard to understand.

One strange thing that I have discovered today is that almost all neuroscientists use "data" and "metadata" as plurals; bioinformaticians use either but tend, these days, much more to the singular.


Databasing the Brain

Am at the "Databasing the Brain" conference in Oslo. So far, we've had a fairly hairy start; the taxi ran out of petrol on the way. We decided to walk the last 1-2km; it turned out to be more like 5-6km, uphill with luggage and a laptop. The guy didn't even apologise or thank us for pushing him of the road.

Still, gave my the chance for a look at the environment which was lovely. We're up in the hills, past a sky jump, pine forest, fresh air. What more could you want (other than time to enjoy it of course).


Garlic Broth

Tried a garlic broth this week, with garlic flakes. Think that this was a mistake; a couple of bulbs of garlic would have been better. Essentially, I fried lots of garlic for a while with a some onion and then some stock. Then added tofu, potato and udon noodles.

The taste was fairly good, although it didn't keep that well. The main problem was the colour; it was pretty palid looking and would have been better with, say, lots of soy in the broth base.

I will work on this; I like the concept of garlic as a main ingredient rather than a garnish.


Train Windows

In the bad old days, we used to get problems with the termpature in trains all the time. They had windows which opened, which we did when it got too hot. In summer, travelling down the line there could be many windows open, blowing air in the carriage.

Thankfully, these days have gone now. The windows have all been blocked up and sealed, because now we have air conditioning. It's great. Even when the weather outside picks up to a scorching 24C, inside the train will remain a comfortable 32.


New Machine

Just taken delivery of my new machine: a Sony TX2XP. It's quite cute. The keyboard takes a little bit of getting used to, as it's fairly small, but it's probably worth the hassle for the overall size and weight of the machine.

In general, it seems a significant enhancement of the previous machine I had. The mouse buttons are nicer than the old one. The power management drivers are cleverer (the DVD still powers off when in low power mode, but switches on again if you want it...although it won't switch off again if you don't). The only real fly in the ointment are the graphic drivers which still don't work properly: they just cannot cope with multiple set ups. The previous version tried to guess what you wanted, but often got it wrong (setting up a project as an extended desktop for instance). This system has some right click context menus, and includes an option to set up schemes, so you can pick what you want. Sadly, it's totally broken. It seems to randomly forget schemes (although they come back later) and, even when it remembers them, it doesn't get them right, leaving the resolution unchanged. Pity, because it's a good idea.

Hopefully, this one will last a little longer than my last one.


What is a unit anyway?

I discovered yesterday that our marvellous Bioinformtics Support Unit has two offices. One in the medical school and in the Devonshire building. More over, it has two people in it.

This leaves the question, in what sense is it actually a unit?


Awards for New Academics

I've been writing up a document for the EPSRC Case for New Academics aware today; it's an interesting award, in that it is a fairly low bar for entry, if you can get the CASE component. One of the odd things about it, though, is that you have to submit the the details of the student before you have the cash; at this stage, obviously, you can't promise the student anything, and not having the cash you can't advertise for the student. Bit of at Catch-22 really.

Some of the other requirements are a bit odd as well, all of which have what I think have unintended consequences. First, you can't have been PI on any other grant; this means that you can't really do collaborative work until you have got the first grant because it will make you ineligable for the first grant. Second, there has to be a maximum of ten years since you PhD. This tends to discriminate against people who have not been in academia continously, either because they have been involved in another career or involved in something else.

The basic idea behind these grants is good; I also understand that the research councils don't want them to be seen as a freebie for new academics. It's a pity that they are causing these slightly strange consequences.


Uphill and down dale

Got through lots today; both went swimming and walked to the top of the town moor because I haven't been there before. Really nice, as is happens. The weather was warm, but with a fresh breeze, generally very good.

I was thinking about how we define racism; many people equate it with prejudice (based on race obviously), but I don't think that this is enough. There needs to be some political or power structure in the way, otherwise it's just prejudice and why have two words for the same thing.

It's often hard to describe the different between the two concepts, but I have a good analogy: is a heterosexual man being sexist when he chooses to only go out with women? Most people would say no, but he is clearly being prejudiced, just not in a way that most would find unacceptible.

Strange thing to be thinkin about on a beautiful, sunny afternoon, but there you have it. When I got home, I ended up listening to Peter Day on in business; I can't see it myself — I'm sure he's well respected but he always seems unincisive, lacking in depth and patronising. A very rare collection of attributes.


But it can't do that

Just tried using a new system for postgraduate admissions at Newcastle. It's built on top of the Universities SAP system, which means that it probably cost lots of cash and barely works. It's taken me about a week to login. Amasingly the system seems to consist of scanning in documents and displaying them as a tiff image, surrounded by enough Javascript to ensure that it will only display with a single viewer.

I went to a talk once by Ted Nelson, during which he slagged of Acrobat. His comments were over the top, but he has a point. Transferring a printed document to screen decreases it's usability. It's the 21st Century people! We shouldn't still be doing this.



I've been having wrist problems recently, so I decided to try a track ball. I've bought a Logitech Marble trackball. It has a track ball and four buttons — two main ones, and two smaller ones which can be bound to different things. The secondary buttons did strange things by default (operating back and forward history in Firefox, and Mouse 4 and 5 in Emacs). So I ended up installing the Logitech drivers to rebind these. Very annoying. As well as mouse drivers it insisted on installing Music jukebox and a desktop E-Bay shortcut! This has to be the most irrelevat co-install ever. The drivers are also annoying; the GUI removes the "pointer trails" options which I generally use and always binds a click on both the main buttons to something, rather than just letting in through to the underlying system, thereby blocking cygwin's middle mouse emulation, for example. I managed to recover this situation with a bit of judicious registray hacking. Pointer trails can be turned on here, and the allowable gap for recoginition of a keychord can be turned down. But, really, should we have to go to these lengths?

Still. my intial experiences with the track ball are good. My wrist already feels more comfortable; it's largely static during mouse use. My accuracy still leaves something to be desired, but it not far behind mouse use already. Hopefully this will improve in time which will mean I can turn up the speed somewhat as well. For those with stiff wrists (oh, er, Missus) a trackball is recommended.


Sad Tidings

I spent the weekend back in Worcester for a sad occasion: the funeral of my Uncle Viv. A funeral can be a maudalin experience, but this wasn't. It was a great opportunity to reflect on my Uncles life. I remember him in his house describing events from his life. Most of these involved his work — he was a train driver — and a lot of them involved incredible feats of alcholic excess. Often at the same time. But he was a much more than this; in his time he was heavily involved in the trade union movement, making the life of other workers better and, crucially, safer. It didn't take long in his presence to appreciate his humour and the ease of his personality; it's perhaps only now, after his death, that I've realised how much his compassion defined his life.

One of this other major characteristics was his ability to talk the hind legs of a donkey; this is something that most of my father's family — including myself — share. An opportunity to see and talk with them is always good; the stand out moment was my aunt telling the most tasteless gag that I am ever likely to hear at a funeral. Excellent!


And a new one

I've borrowed an old IBM laptop to be going on with. It's fine. Nice big screen, good hard drive. Slightly broken keyboard and a wireless card that only seems to work at 11M. I'm going to get one of the small Sony 11in laptops in the long term though. This machine is something like 3kg which is way to heavy.


And my laptop croaks

Yep, shortly after getting broadband at home, and a funky new NAS box, by laptop died. It had been getting increasingly slow. I had decided that this was probably because it was having a Microsoft Moment, although there was possibility that physical trauma was the cause. So, I tried a full reinstall. This went okay, but didn't solve the problem.

On Saturday, while drunk, I discovered that it was only registering half a gig of memory, rather than the 1G it should have. So I took the memory off, blew the contacts clean with compressed air and reinserted. And now it won't boot. Worse, I have now discovered it should only have half a gig of memory.

Never, ever fiddle with hardware when drunk. It's only going to end in tears.


Breaking an Identifiable Silence

After weeks of not much of interest happening, there was a flury of activity today on the Semantic Web for Life Sciences mailing list. This was largely the fault of Alan Ruttenberg who used the two words which on their own are most likely to cause an argument between bioinformaticians — "identifier" and "standard".

How depressing it is that we are still having these discussions after so much has been achieved. Bioinformatics will use a standard when it suits them; people have been active in using GO or MGED. Identifiers, however, still remain a problem.


Billy Bragg and Seth Lakeman

I've seen Billy Bragg before, but never at a gig that I've had to pay for. He gives value for money, it has to be said, and played a good long set; he still can't sing, and it still doesn't matter that much.

The stand out performance, though, was the support which was Seth Lakeman; I've rarely heard such an intensely rhythmic band, and certainly not one playing on acoustics. Be looking forward to seeing them live at a smaller venue.


Tiscali arrives

Finally got my broadband connection. An interesting experience; spent 20 minutes fiddling with it, and failing to get a connection before I gave up and phoned the support. They were alright — the modem drivers needed re-installing and the windows config needed doing manually. Two days later, I got a Linksys ADSL Modem/Wireless router. Ironically, I managed to get up and working in five minutes.

My file splitting scripts didn't work initially. The problem is that Unison uses temporary file names while copying and this includes directories. So if you transfer a single directory containing 2G, for example, Unison will use a temporary directory till it has the whole lot. So I tried rsync instead; this worked well up to a point — about 2.4G as it happens, where a bug causes it to block.

Finally, I worked out how to get Unison to work — firstly, I run it with

ignore = Name {*.*}

This matches all the files (and not directories by and large). So the directory structure gets transferred. Then, I run Unison again; now it transfers the files so you get a restart with the granularity of a file. For really large files, I can still use my split file scripts.

Having said this, I am getting very variable download rates from the ADSL — 1.5Mbs and more at night, but during the day rarely more than 500K. To be expected, I supposed.


Cross-Cutting issues

The workshop has today been discussing cross cutting issues between neurosciences and systems biology. Funnily enough, many of them seem fairly familiar: how to visualise complex, multi-dimensional data; how to combine and standardise the representation of data; how to combine models; how to enable scientists to work cross-disciplinary; and, how to train students to work in the area in the future.

One of the main differences seems to be a cultural differences: if you put two bioinformaticians into a room, they will publish a database; in neuroinformatics this tendency doesn't appear to be there. I think that part of the reason for this is the lack of an obvious common standard representation. In bioinformatics, we worked from the DNA and protein sequence outward.


Systems Biology and Neuroinformatics

At a workshop in Edinburgh today. Thought it would be a good ideas; the CARMEN project is coming up so having some understanding of neuroinformatics. As for systems biology, thought I'd like to fail to understand some more people telling me what it actually is.


The Morning after...

Yes, now I am 35. Years ending in 5 and 0 are always difficult ones. This one makes me, now, well on the way to middle age.

Ah, well, there's nothing that I can do about it, so why worry?


Walking and Cleaning

While I was out walking yesterday, up around Northumbria with my friend, Ian, I realised two things: first was that Ian and myself hadn't been on a walk together since before I went to Edinburgh, more than fifteen years ago; second, that I didn't know how to clean the pipe of a water skin. These things are great in general, but can be tricky to clean, and you have to remember to empty the water and dry them. Last time I walked, I left some water trapped in the pipe and it went green. How to clean it?

So, here is my solution: cut a piece of cotton thread about three times the length of the pipe; about half way down tie a small piece (about 2cm) of hemp string or something similar; feed the end of the thread into the pipe — getting a couple of cm's is easy, more is hard; now, dribble water through the pipe. The point is that the flowing water removes the friction between the thread and the edge of the pipe, and slowly pulls the thread through; you just have to feed the slack. When it's all the way through, you can pull the string into the pipe; again, keep the water flowing or at least full of water. You can use the string to scrub the insides.



Wasn't sure about this one. It was an entertaining watch, I suspose, although I've got to a point in my life where I find Jack Black irritating rather than mildy amusing. Still, John Cusack is charismatic enough to rescue most films, it's full of pretty women and has some wonderful songs in the soundtrack which have been moldering in the dust of my record collection for too long.

Strangely, reading the credits, I noticed that the executive producer was Alan Greenspan. Good to have strong support on your side.


Bhajee on the Beach

I've only ever seen the last five minutes of this film about a decade ago. I hadn't realised that it was written by Meera Syal. Great film; funny, with nice observed social commentary and a few bits of the bizarre. It feels slightly dated now, but seems to improve with age; it now reminds me of history as well.

After that, I watched the X-Men 1 film; perhaps a strange choice; it shares one thing, though, with Bhajee on the Beach which is an excellent ensemble cast. I think I prefer this sort of film to the big star vehicle which is too common these days.


Aloo Gobi

Bought a copy of Bend it like Beckham a while back; personally, I disagree. I'd rather be able to cook Aloo Gobi than kick a curve ball. Fortunately, I can, I did. Yeah, it was alright.


Splitting Files

I want to use Unison, the file synchroniser to move files between home and work, when my broadband comes; this means I can put files into a transfer space, and remove them either side: I won't have to clean up twice. There's a problem though: Unison can't restart an interrupted transfer. This is a pity because it uses the rsync algorithm and copies to a temporary file; it should be easy enough to restart the transfer. It effectively blocks using Unison over the (slow) broadband that I am buying, at least unaided. So I've written some scripts to copy and split files into small bits. I'll release them to the website in a few days time. Can't believe no one has done this before, but I couldn't find anything.


Edinburgh Past

Fell across my old flat mates tour of Virtual Edinburgh today. I had some good times in the flat there, although it used to get into a real mess. This picture of the bathroom; the bit which says "if anyone stays in too long" largely refers to me.


John Renborn and Robin Williamson

I've seen John Renborn a number of times, but never Robin Williamson. Had seats in the front row, so it lacked the coldness that you normally get in the Sage. The music was beautiful and melodic, but the gig as the whole lacked enough variation. John Renborn did one Booker T number, for instance, which was fast and the audience went wild. Robin Williamson provided some good chat between songs, although he played far too many instruments; his sound was a bit ropey as a result.


Shipping News

At christmas, the stand out film for me was "The Shipping News". So I bought the book. Immediately after this, I mentioned the film to a friend; his response was "don't bother with the book.

Actually, I quite enjoyed it; there is less Hollywood-ism (i.e. the lead characters arn't good looking); the book has more time to meander than the film, which it benefits from. I find it a little overly stuffed with metaphor and similie, which at time jarred a little; othertimes, it was highly effective ("the sky was bruise grey"). Combined with her tendency to use verbless sentances ("The smell of sea damp and paint") gives the book a slightly breathless feel.

Generally recommended. Particularly, as it has lots of short chapters, which makes it good for reading in the bath.



Decided to get broadband for the house; bit of a nightmare; there are so many variables that the different packages are hard to compare. Bulldog appears the cheapest at a tenner for 8Mb, but isn't available here. Irritatingly, they over a slower package for more. CarphoneWarehouse announced a new package today, but this involves the phone and has an 18 month tie in, and a 30 quid connection fee. Currently, tiscali appears the best, though. It's slow (1Mb), but cheap and uncapped, and seem to have good house moving policies. The only problem is that they don't do static IP's. I think I can get around this, with various NAT fiddlings, but it's not-trivial.

This is all a pain; there is too much choice here, too many options. This seems to be true in general for telecoms. The problem is that it's just too expensive at the moment, so people are actually forced to care about these differences. Give it another year or two and I think the prices in general (for non-mobile anyway) will come down enough, to where it doesn't matter. At least, I hope so.



Spent some time in Manchester; I went down mostly for the BioPAX meeting. They are hoping to use the formal semantics of OWL, within the BioPAX encoding, which the current versions do not. I think that the difficultly is going to be deciding what should be represented in OWL and where is should be used as a surface syntax.

It was lovely to see everybody again. I even got to buy some cake as I had a paper accepted last Wednesday.


Talk to the Head

Got a reply from the Business Directorate in my attempt to get a signed copyright waiver. I tried the technique of writing to the head of the department which seems to have resulted in a reply. Actually, it produced several replies, from the head, and the next down, and then the next down again. Fingers crossed we will be there soon.


Advantages of Open Access Publication

I realised today one of the more obscure advantages of Open Access publishing. This produces a major change in the economics of the scientific publishing, which is that the payment happens during the publication, rather than before reading. This is entirely wrong, it seems to me. Most scientists spend far too much time publishing and not nearly enough time reading. Making people pay to publish, but allowing cost-free reading should help to redress this balance.


Choose your Friends

I decided, yesterday, that I would let my brother in on the journal; in general, I haven't been telling many people about it. While I might have been hoping that the world at large was about to discover a Samuel Pepys for the new millenium, I wasn't entirely to give up the day job. Still, I might have hoped that my brother's first opinion hadn't included adjectives such as "pompous" and "muiresque" (as in, like Frank Muir).

Well, what can I say? Ever has the path of the true genius been strewn with the yapping and braying of those snapping at their heals. But I shall continue, I shall persevere and broadcast my words to the unfeeling ether of cyberspace that surrounds us!


Top of the World

As have others, I said in the past that I don't really like country music; more recently, I realised that there are bits of it I do like, so I try to remain open minded. I happened across the Dixie Chicks "Home" album; I remember they had a lot of hassle over Gulf War II, which is why the name stuck, so I gave it a listen.

It's great; there's some fast and furious bluegrass playing, so pop songs, some delicate ballads. And one or two rather crap love songs. Ah well. Interestingly, all the stand out songs, for me anyway, are covers. I've worked out one, Top of the World. Funnily enough, the middle section has the same chord change to a very bad, slow, folkie version of "Little Red Corvette" that I used to play poorly many years ago.


Video Nasties

Following yesterdays road scraping, I've decided to commemorate the occasion with a gallery, named after a band I've been getting into recently. So, I proudly announce the Bruise Armada. I will update it over the couple of weeks.


Curried Rice

Have been suffering from a problem; due to some over-exuberance, I've had to eat with a teaspoon for the last few days. Fortunately, on sunday I'd cooked some bulgar wheat with chickpeas. Today, was curried rice.

Very simple: garlic flakes, oil, pepper, black mustard seed, all fried. Then add rice vinegar and some soy. After a few minutes of frying put in a enough rice and fry it drish, then add enough water. Finally, spice with an Oxo cube, cumin, coriander, turmeric and add a small amount of tomato puree and chilli sauce.

To give it a bit of bulk, I added peas, broad beans and some quorn chicken. Turned out rather well, as it happens. Takes about 15 minutes in total.


Young at Heart

Well, having felt middle-aged in my last entry, today I feel rejuvenated and young. Just to prove that I can be foolhardy and idiotic, I fell of my bike during an overtaking manoeuvre of quite staggering incompetence. It's nice to know that I can still engage in fits of youthful over-exuberance. Kind of knackered the bike up though.

The image is included as my contribution to medical science. Ouch. Thanks is due to man I was overtaking, who helped me up; particularly nice, as I almost bought him off.


Wee Jocks Lament

Got the second Hamish MacBeth DVD today. Bit irritated to find it short one episode; ho hum. Watched Wee Jock's Lament; excellent episode. It mixes humour and death, killing and repentance, and throws in ghost sub-plot. In lesser hands, it could have been cheesy on a stick; but it's so lightly done that it worked; the ghost appearances really freaked me out, the pain of the loss touched me, and the laying of Wee Jock's stone had me in tears. Did the BBC really never repeat these?


Forgotten Possibilities

I'd totally forgotten about the upcoming John MacLaughlin gig; in got tickets on the day of the gig. Glad I did. He was playing with Shakti — mellow, acoustic (well except for half the instruments), Indian.

If you'd only heard him recorded, you might feel that a John MacLaughlin gig is to be impressed, rather than entertained. The speed, fluency and virtuosity of the performance is astounding; but on record, you wonder whether there is more. This music needs performance, though; live, the flurry of notes blends, the music Star breathes; it's hypnotic, engrossing, compelling and, frankly, exhausting. I came out with knees hardly working.

I was slightly irritated by the formality of the setting of the music, though: the introductions were Hollywood-gushing; a 2 hour set with no interval was bladder-bursting.

I got the metro home; bought a ticket which I didn't need as the SAGE tickets count; took till two thirds of the way across the river toward Gateshead, before we realised we were heading in the wrong direction. Senility approachs


Lubricating Middle Age

Yes, today, I have officially become middle aged; I have reached that time in life where I have had to buy my second can of WD40. For some people, WD40 is a passing thing; mechanics get through tons of the stuff. For most of us, though, it's that essentially accessory that you can't do with out, but rarely need. Losing the straw can be a highly traumatic experience, which can leave you scared for minutes afterwards. Your first independent can is a rite of passage, a move to adulthood.

It's, perhaps, a sobering reflection that at the current rate of usage, I will own two more cans before I leave this mortal coil, or have no further use for the stuff.

Still, bike's running better, so mustn't grumble, eh?


Waving at Copyright

I've been trying to get the University to fill in a copyright disclaimer for the Free Software Foundation. This was painful at the Manchester and looks like it's going to be similarly so here. So far no one has any clue about who I should even email; I'm working on the business directorate who are supposed to be in charge of IP. So far, they are ignoring my email; soon, I am going to go and sit on their door in person, till I get a reply.

This doesn't bode well though. When I tried to get a login for, it took about a week and a paper chase of 6 people before I finally got to the one who knew.


Pension Costs

"The public sector does not generate wealth for UK plc, only spends the wealth the the PRIVATE sector makes for the country. We the tax payer funds the public sector pensions and therefore I feel that the pensions playing field should be level for all."

Today, UNISON were on strike over changes to their pension rights. The comment above came from the BBC news website. It's an odd point of view; the private sector magically creates wealth, the public sector spends it. So, someone on tax exempt business lunches is creating wealth — at least if they are private sector. I, on the other hand, when researching new knowledge that enables biologists to do new things, am just a sponger, because I work in the public sector.

At least now I understand the PFI: while the NHS would previously have built hospitals using public sector workers, thereby consuming wealth, now they use private sector workers, thereby creating wealth; this is quite remarkable, given that they are doing the same work, paid from the same source, and achieving the same end. Whoever came up that idea must have been very clever indeed.


Multipath Unison

I'm a huge fan of Unison, the file synchroniser. I use it religiously; half of my system is based around it. It has a few quirks, however, and today I fell into one of them. I'm sure I've been here before, but I couldn't remember the cause.

Essentially, it gives a cryptic message about the transferred file disappearing. The basic reason is this; Unison can't cope with a path been included for synchronisiation twice; it twices to synch the file twice, and each time messes with the other.



Well, two gigs, and one night of extreme technqi-ness, had left me tired, so I spent the weekend doing very little; more vids.

I'm trying out online DVD rental and managed to get hold of a copy of the first season of Hamish Macbeth. I was a bit nervous: when this came out, I thought it was great, and I didn't want to find out that my memory decieved me. Sure enough, it was fabulous; funny, tightly plotted, closely observed, cynical and black.

The rest of the weekend has involved stupid quantities of Star Trek — also good, but continually spoiled by the tendancy for the script writers to want everything to turn out swimmingly. And, of course, Wesley Crusher who is as irritating now as he was then.


Warm Stew

Simple meal today; onion, a suede and quorn mince, fried for a while (yes, with chili and garlic flakes), then simmered with tomato puree, and thicked with Oxo cubes and gravy granules. Add mashed potato, peas, beans and spinach. Thick, warm and filling. Pity, really, that I got around to this just as the weather is starting to get warm.

And, yes, it should have been a pie. I've clearly been scared by the pastry experience of last weekend.


Salsa Celtica

Thursday night was Salsa Celtica at the SAGE. They're a large band which combine, obviously enough, Salsa and folk. They were absolutely amazing; the two forms of music blended naturally; perhaps, this is not so surprising as they are both hard core dance music. Rhythmically, the mix was better than melodically; I wasn't sure about the Northumbrian pipes which are difficult instruments. The chanters are nasty to tune at the best of times.

This was also the first time I've been in hall 2 of the Sage. Much nicer than hall 1; oddly, though, despite having a dance flour on the lowest level, they choose to lay out seats right at the front; get up and dance guys!


Contract Law

Was good to see some friends from Manchester up north. Michael Parkin and Dean Kuo came up and talked about a protocol that they are developing which is based around contract law; the idea is that this is a form of negotiation which they should just be able to lift and reapply to computer science.

It was a good talk which caused lots of interest. Indeed, I was surprised that they got through all their slides; there were so many questions; felt like much more of a discussion session.


Freaking Out

Graham Coxon played the Newcastle Students Union last night. I felt nice and old; seemed terribly loud. Had a great time, though, bouncing up and down near the moshers at the front. Very talented guitarist, excellent band. I think he lacks as a front man: I always liked a bit of repartee, myself. Also, you have to wonder how long his disaffected youth lyrics are going to work. Noticed that James Taylor Quartet are coming up soon; I'll be there.


Dumping Outlook

It was hard, tedious work, but, today, I finally dumped Outlook. Nearly six months of using it and it was driving me mad. No decent threading, slow interface, battery sapping processor requirement and a wrist-aching dependency on the mouse. Awful, truely awful.

So, it's back to Gnus.

The irony is, this is all unnecessary. Our local systems people, ISS, have a daft policy of actively trying to stop people using other clients. This is to reduce the amount of work they have to do, and to encourage the use of Outlooks shared calendars. So, they've switched the IMAP interface to Exchange off. Result, if you want the calenar, you have to use the Exchange email, and therefore, outlook; in my case, the cost of UI is such that it's not worth advantage of the shared calendar.

It's good to be back in the rapid environment of Gnus, though; I can move around quickly, I don't need the mouse and I can control what the email looks like. As a side effect, I'll be back in a programmable environment which will be great for returning coursework and the like.


Teaching creationism

Should we teach creationism in science? I have to say, I think, we should. I don't like the notion that you should separate out science from the rest of the world; is it alright to teach creationism outside science, but not in it; should we not be teaching, within science, the impact that science has on society?

I'm happy for science to stand up on its own merits; by attempting to protect it from creationism, we are also preventing from describing its strength.


Sausages and Beans

Decided to do sausage rolls and beans after a hill walk on sunday. Nice idea, but I turned out to have no beans, no self-raising flour and forgot to put fat into the pastry. The pastry was solid. The sausage actually worked okay, though. Some dodgy Sosmix from down the road. Just add boiling water. I put in spinach and garlic flakes into the water first, and lots of pepper.

Pretty good, actually.


Weekend of Vids

Future generations may call it a DVD session, but to me they are still vids. And I've watched quite a lot this weekend.

On Saturday, I went around to Dan's; he'd plugged his stereo in and projected the image on a wall, which worked well. We watched some Frazier, which I haven't seen for ages; it was good, the dialogue was fast and furious; sadly, for the authors, perhaps, the funniest thing was Daphne's old boyfriend, and his unfortunate attempt at an English accent. Only Dick Van Dyce ever said "lov-er-ly". After that, we watched Serenity. The cinematograph was good to watch, some reasonable fight scences and lots of very beautiful actors; ultimately, though, I didn't care about any of them.

The stand out vid, though, was today; I watched Sleepy Hollow. I didn't know it was a re-working of a fairy tale, Great film: Tim Burton's visuals were stunning, Miranda Richardson was outrageously evil and Johnny Depp's cheekbones were incisive as always.


Mutliple networks

Windows seems very confused; if you have two network interfaces, one with an internet connection and one without, windows seems unable to work it out; sometimes, it tries to access the world through the wrong one. Confusing. Answers on a post-card, please.


Irritating Interfaces

I've been using iTunes, recently, to play my music. It's quite a nice interface; it's sad, however, that it's crippleware. It doesn't include other peoples' shared music in its "recently played" or "most played" lists.

It also lacks a "watch directory" option; if you add music to a directory, you have to add all the files individually: add the directory, again, and everything becomes duplicated. Picasa has this, why not iTunes?


Think Twice

I've been listening to Groove Armarda a lot recently; their "Love Box" CD is phenomenal. The stand out track is "Think Twice". I was surprised to learn that the vocals where by Neneh Cherry. I remember when I first heard "Buffalo Stance" and, then, later "Manchild" a decade ago. It was great to hear her rich, sultry voice again. It draw you in; its warmth envelopes you; removes you from immediate.


The Economics of Science and Teaching

Had a slightly daft conversation in the pub last night, covering science, industry and economics. As is inevitable from such a conversation, this failed to reach any big conclusions.

Thinking about it later, though, I've decided that research and teaching have fundamental economics. Thinking back into the past, my educational experiences have all been valuable to me; just not that valuable, at least not for a given piece of teaching. Teaching, then, seems to pay off, in that it's for a given course you chances of getting some return are high, but the return is likely to be small: anything you learn you are going to use, just not that often.

Science and research in general are very different; most of the research done in the world, more or less by definition, comes to nothing at all. Some of it, however, pays off in a huge way. Occasionally, a small piece of research changes the world. So, the chances of getting a return are small, but the potential return is huge.

It's odd that two such different activities have been combined in the education sector. From a practical point of view, the combination seems natural to me; my research provides the foundation to my teaching. But from an economic point of view, is the combination of the two sustainable?


Aduki beans

I used to think that aduki beans were a joke from the Beano. When I was a kid, Baby Face Finlayson used to eat them after coming up with some dastardly scheme.

More recently, I discovered that they were real. So I tried cooking them last night. Rather nice, as it happens.

The meal was this:

  • tofu
  • red onion
  • garlic flakes
  • rice vinegar
  • soy sauce

All of this was fried in garlic flavoured olive oil, tofu first with the soy and vinegar till brown and then all the rest dumped in. This was eaten with rice, with peas and broad beans, with a light drizzle of liquidizied chilli.

Very nice as it happens. The aduki beans taste like a cross between baked and kidney beans, but didn't overwhelm the rest of the meal.


Bike Lane Disaster

I don't like the bike lanes that I ride on every day to work; it has to be said that there are many worse ones around. The BBC News site had a great set of photos of these today. It's a pity; bikes lanes are normally put into to fulfil government targets, but not actually to be useful. A little more care would improve the network's usability enormously.


More curry

Decided to try the curry house from a few nights ago, as I was on the Quayside last night. I think it's called "the Rasa" but I forgot to write it down. Sadly, it was suffering from the Newcastle disease — it was fully booked. I don't understand why this is such a common problem here, but there you go.

Instead, we ended up next door at Vujon. It was okay. The seafood angle was well covered, but the veggie options were poor. I ended up with the set of side dishes option, which were adequate.


Wave Power

"Unlike solar, or wind power, the tides move all the time"

Interesting story on the news about the first commercial wave power system. This is happening in Portugal, despite the technology being developed in this country because Portugal gives preferential treatment to energy from renewable sources.

It's great to hear that this is happening, regardless of where it is happening. It fits quite nicely with stories earlier in the week about gas prices. Currently, the problem with all renewable energy supplies is there high, up-front costs. But, energy supplies are getting less dependable and more expensive with time, and renewable technologies are getting cheaper as they are moving toward mass production.

The quote is from a listener to the radio. I'm not sure it makes sense. The system was a pelamis system (pipes which hinges, which pump hydraulic fluid, while they bend). As most waves occur as a result of the wind, rather than tidal movements, the pelamis system would be susceptible to becalming; just not very often.


20060313 Versioning Madness

Started to have a look at Darcs today. It's one of the first distributed version control systems that I've looked at in detail; I couldn't see how they worked myself, but it's not that difficult. Everything is a branch and you pass patches around; obvious — at least, once you think of it.


Broke my NAS

Spent about an hour trying to work out why the aforementioned NAS box was totally failing. The ftp server seemed to be working, the machine seemed to be identifying itself.

Turned out to be the firewall. Windows can cope without a call-back it seems. It looks rather like this was also the cause of poor performance on small files. I've managed to get my network card up to 30% utilisation; saturday it was rarely more than 2%.


Garlic Flakes

Finally got around to buying some garlic flakes that I saw being used in t a resturant a short while back. Combined with a bit of chilli, as well as being garlic flavoured, this are actually quite hot.

Cooked them with some potato, tofu, red onion and bulgar wheat. Very nice indeed.


Fat Men in Saunas

The image of a fat man in a sauna is a bit of stereotype. This never made a lot of sense to me. Surely, thin men are as likely to go to a sauna? Think I finally solved this conundrum today: fat men have a good layer of insulation around them; so, they will heat up more slowly than otherwise; which means that they will be in the sauna for longer. Which means that, at any one time, there will be an over-representation of fat men.


Teaching Clusters

Finished teaching today for year; well, ignoring the research projects, which might be a mistake. I don't understand exactly why I find the teaching so tiring; probably the main reason is getting on top of so much background material. Still, it's been a good thing; I've needed to get on top of MIAME for quite a while.

The lecture actually went okay. Rather than go through the data model, which would have been dull, I think, I did a "clustering exercise", which I learnt at last weeks LSI meeting: everybody wrote down terms on post-it notes; then, they get arranged on the board, into related clusters. In the end, we got clusters which fell neatly into the six points from the MIAME checklist. Fairly pleasing, really.


20060309 Vedna

Went out for a curry tonight, with an old friend of mine. Fortunately, he knows lots of nice places to eat in Newcastle; this is good, because, currently, I don't.

I can't remember the name of the place, but it's near the Quayside, and rather pink. But the food was excellent. We had a daal, a strange pancake bread, a cabbage dish, dosa and some vedna. I've been a fan of dosa for ages, since discovering them in the Punjab Tandoori in Manchester. I've only had then in one other place, so it's great to find another resturant cooking them. I even tried making them for myself once, using some of the wonderously named "Mr Git's Dosa Mix". It never worked.

As well as his dosa mix, Mr Git also makes vedna mix. I did buy some, but never tried it. So, this was the first time I've actually got to eat them. They were great. A light donut made out of lentils.

Afterwards, we went back to the pub and I almost fell asleep. I hadn't realised how tired I was.


Teddy Bears and Swordfish

I thought, last night, that I had seen the clear winner for my weekly "Most Surreal Experience" competition. While sitting in the pub, looking out of the window, two blokes walked passed carrying between them a 6ft, blue, plastic swordfish.

However, today, this was defeated: the swordfish was robbed. During our strike action, we had the traditional rally, where people stand in front of a microphone and talk at other people who are feeling cold. For some strange, ill-conceived reason, someone came up with the idea of bring along entertainment in the form of a left-wing accordionist singing, among other things, a strange rendition of the "Teddy Bear's picnic". The middle part involved a Freudian analysis of his childhood, during which he swore and almost got arrested for a public order offence.

Strange. Very strange.


Veggie Mixed Grill

Went to Bob Trollope's today. It's a veggie pub, near the quayside. Went there before, but got confused — I ended up looking at the menu of the pub next door.

Wasn't bad at all. Had a pretty good menu. As I'd been standing outside in the cold for most of the day, I went for the mixed grill. Was alright, but I think they need to make it a bit different from the meat version — it was too dry. I couple of pots of dips (a light chilli sauce, some brown sauce and something a little sweet, perhaps) would have been perfect.

Still, it's a pleasure to be in a veggie place, with lots of choice on the menu. It's not been that easy in Newcastle.



"They get great working conditions, extended holidays and commission from all the books they write", a student fumed

This quote was from the local student newspaper.

It's perhaps not surprising that students (like most of the population) are unaware of what academics actually do. Teaching, itself, takes a lot of effort, time and thought. Few students wonder where the knowledge that we try to teach actually comes from; it's in the creation of this knowledge that we spend the rest of our time on. It's the reason that we don't go on holiday, when the students go home.

There is a lot of cynicism among academics; when you feel part of the degree awarding, paper writing, grant applying treadmill, it's not that surprising. But academics are hamstrung in their industrial dispute not by their cynicism, but their naivety; most of us still get a thrill and excitement out of our subjects; the pleasure in the knowledge that we teach, the excitement of extending it palpable. It's for this reason that most of us work silly hours. It's the reason that most of us will spend the time on strike working at home.

We find it hard to withhold our labour, because in doing so we hurt ourselves as much as we hurt others.In our market driven society, the value we put on the process of science subtracts from the value that society puts on us. Despite this, I will go on strike tomorrow; perhaps I am naive, but perhaps I like it this way.


It Never Rains

Been a bit strange, recently. I'm an occasionally emacs hacker. My last big package, pabbrev however was first released about three years ago, and hasn't had a new version out for at least a year.

In the last week or so, though, I've had a flurry of fixes for it, even added a new feature. More over, a new package called "predictive" which is similar but more powerful (good!), but more complex (bad!)o has been released. Added to the work done on muse mode which I use to publish this journal, I've been deeply embroiled in lisp.

I never understood this sort of synchronicity.


Linda Smith

Listening to a special edition of the News Quiz being played as a tribute to Linda Smith, who died earlier in the week. A sad loss — I loved her rambling style, her ear for the bizarre, her inventiveness, while she still managed to be incisive about the issues of the day.


Polenta and Parsnips

Having dug out my old recipe for bulgar wheat, I've been going all cereal. So I bought some polenta. I've never tried this before. It's like cous-cous, but a bit finer. You cook it for a while, then it goes solid.

It's relatively tasteless, but is spices up well. I did it with parsnips and potatoes that I'd lightly fried with lots of spices.

It was alright, but I need quite a bit more work on the polenta. Less water, I think, more spices.


Top Down vs Emergent Standards

There has been an interesting discussion on data standards for systems biology. This theme seems to repeat itself again and again. Despite the obvious difficulties in getting scientists to work together, slow, steady, building of standards with as broad a consensus as possible has to be the best way of doing things.


20060228 Life Sciences Interface

Went to an interesting workshop on EPSRC's LSI programme. One of the interesting things which came out of this, is that most people who actually have LSI funding are not aware of the fact.

I was a bit surprised about this. So were the people in charge of the LSI. However, they later admitted that the main reason for this was probably that they had made a strategic decision not to tell people when they got funding.


Religion and Cricket

Caught an announcement on the radio that the daily service was being moved to make way for the cricket. There is a certain irony that religion is being moved out of the way for sport; having lived just down the road from White Hart Lane, then Maine Road, and now overlooking St. James Park, this makes a certain amount of sense.


Biriyani Toast Topper

I bought some soya mince the other day, mostly for old time sake. Soya mince much like the larger equivalent, soya chunks, are fairly horrible. They tend to be overly chewy, with a slightly unappealing texture. But they are cheap, and about 50% protein. I used to eat lots of this stuff when I was a student and then stopped, because I could afford nicer food. But I saw some the other day, and remembered that I had one dish where it was quite nice. This is it.


1 Red Onion
Handful Soya Mince
Handful Rice
Tomato Puree
2 potatoes



Garlic Puree
Various Curry Spices


Essentially, this is your basic curry — fry the onions, then add garlic puree. After it's cooked for a while, add some lime juice, then cumin, coriander, tumeric and any other spices you fancy. This makes it pretty dry, so before it burns add tomato paste, and then water. Today, I also washed added some garlic pickle. Milk is good as well. Cook for about 10 minutes. Then add the soya mince.

While this is doing, parboil the potatoes, then add them to the curry. Follow this by part cooking the rice in the same saucepan, and add this to the curry.

The combination of the rice and soya mince will soak up a lot of the moisture. Add a bit more water if needed: there should not be much left by the time everything is finished; it's supposed to be dry.

At this point, it tastes okay, but sort of wish you hadn't added the soya mince. But this is the good bit; make some toast, then spoon the biryani on top of it, and stick the whole lot under the grill for a couple of minutes and serve.


Thoughts on a Thesis

The Semantic Enrichment workshop has left me thinking about the presentation of science. The thesis or long dissertation of post-graduate courses, is surely one of the oddities of the scientific education system. If you read "Origin of the Species", and other literature of the time, with its slow, gentlemanly meanderings, then then, perhaps, it makes sense. But, in this day and age, almost no scientific research is publishing in long-hand, book form. Everything happens in the papers. Even our books are normally a collection of papers.

So, why do we force PhD students to write a thesis? It clearly is not the best training for what is to come after.


Cats in the Rain

Watched Breakfast at Tiffany's today. It was great. It only feels a little aged, mostly in the styles and some of the attitudes, but the core of it remains. Audrey Hepburn is stunning and George Peppard endearing — you want him to succeed — although you keep expecting him to pull out a cigar, smirk at the camera and say "I love it when a plan comes together".

As it happens, he gets the girl, so I guess it does.


Page by Phillip Lord
Disclaimer: This is my personal website, and represents my opinion.