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 an…

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. Originally published on my old blog site.


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. Originally published on my old blog site.

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 …

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 exclud…

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 it̵…

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. Originally published on my old blog site.


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. Originally published on my old blog site.

Neuroinformatics 2008Day 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! Originally published on my old blog site.

Neuroinformatics 2008Day 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 c…