An Exercise in Irrelevance

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.

Published by hand from my old blog

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.

Posted by hand from my old blog site

"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.

Originally published on my old blog site.

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.

Originally published on my old blog site.

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.

Originally published on my old blog site.

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, http://www.cazy.org), 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.

Originally published on my old blog site.

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.

Posted by hand from my old blog site.

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.

Originally published on my old blog site.