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 u…

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. Originally published on my old blog site.

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 lett…

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. Originally published on my old blog site.

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 li…

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. Originally published on my old blog site.

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. Originally published on my old blog site.

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…

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. Originally published on my old blog site.

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. Originally publis…