Semantic Web for Neuroscience, Alan Ruttenberg

This is a live blog from Neuroinformatics 2009. Creative Commons is based around issues with data and copyright, trying to change the idea that not sharing is the default. Science Commons looks at the issues specific to science. Semantic web in a nutshell; adds to web standards and practices encouraging, common naming, ontology development, expression in knowledge representation language, easy integration over multiple sources, works both inside and outside the organisational boundaries. Why should you want this? Network effects, people can use their own skills, and combine knowledge from many different sources. Provides efficiencies at the global scale. Copy and paste for the semantic web; a mashup with knowledge from Allen brain institute, and google API. Had to screenscrape Allen brain …

Data Integration from genome to phenotypes, Shankar Subramaniam

This talk was given as a keynote at Neuroinformatics 2009. This is my first attempt at live blogging a conference talk, so please read it in this light. There is an overlap between neuroinformatics and bioinformatics; one example of this is the necessity for data integration between the two. Looking to the future; suggests that every database will have a canonical atlas; high-throughout measurements; dynamic live-brain imaging and mesoscopic biology; relationship to disese and pathology. First step was taken by Allen brain atlas, to expression of genes to atlas to be of any use. Altas is now linked out to pretty much everything else; mostly through genes and gene IDs. Example of systems biology approach to prion disease --- injected prion into a variety of different mouse backgrounds. Look…

Neuron and Network Stability, Astrid Prinz

This is a live blog from Neuroinformatics 2009. Neuron systems are incredible stable over time. Looking at a number of systems, including pyloric pattern generator --- stomachs in crabs (?). Is a pacemaker system; it's very stable between individuals and over time. Despite this, for example, the maximal conductance in the neurons varies pretty widely. How come this variability doesn't affect stability? Have generator a single compartment model, looking at 8 dimensional parameter space and making a big database. Trying to replicate the variance that they see within the biological systems. Tend, with their model, to get similar output for these different conditions. Conclusion of this is that neuronal system have a large solution space within which they maintain their functioning. Question, …

Pilsen, Czech Republic

I've just arrived at the conference centre in Pilsen for Neuroinformatics 2009. I got into Pilsen last night, exhausted from the flights and lack of sleep, especially after Science Online. Ironically, I was so knackered last night, that I was in the bedroom by 10 which, follow the traditional hour of fiddling with the aircon to get a reasonable temperature, meant I still got a good nights sleep and managed to get up early. To the point that my phone alarm annouced "It's time to get up", loudly in the taxi here. Pilsen (or Plzen) is famous as being home to the lager. If you didn't know this before you got here, you will after. I'm staying in the Hotel Angelo, which is near the middle of town and right opposite the brewery. Last night, was Pilsfest --- yep, land in Czech and there …

Installing Vista

This year, our clusters are going to be moved over to Vista, so I've decided to downgrade my windows box from XP to vista. It's been an inevitable fun-filled afternoon as a result. Tried a remote installation to save the effort of finding disks. Unfortunately, we tried an installation which booted into Windows 7, and then allowed you to install vista from there; this results in a mysterious 100M partition for use with bitlocker; vista doesn't know about this, so mounted it as D drive and, as it's marked as a system partition, you can't change this. Three installations later, it was gone, and Vista is installed. Next up, install synergy. Turns out that this is hosed because of UAC --- the Vista access control. How to Geek was very helpful, although their technique doesn't completely work. I…

Science Online London 2009

Came down to London last night; forgotten quite how much I dislike this place. Within 10 minutes, I found myself turning into a miserable enemy-of-humanity, having experienced the isolation and rudeness characteristic of the place. Of course, it has to be admitted that the first (re)experience of London involves travelling in the tube, at 5.30, with luggage. Truly, London at its worse. Still, spent the evening, outside the pub, with Aengus Stewart from CRUK; highly entertaining discussion, which is, I guess, London at it's best. (Slight pause here...​Duncan Hull keeps leaning over my shoulder commenting on this post as I write it...​this is not how it supposed to happen, we're supposed to use the internet!). The conference is at the Royal Institution --- yes, finally in the lecture theatre…

Avoiding the Upgrade Problem

I've generally been reasonably impressed with wordpress since I moved to it from my old, emacs-driven system. It seems to work mostly and it's reasonably easy to manage. One problem has been the regularity of the updates; worse, they all tend to be security updates (2.8.4 was to correct a problem where a crafted URI allowed overwrite of the admin password). So, you have to update. Often. Fortunately, wordpress provides an automatic mechnism for achieving this. Less fortunately, it doesn't work for me. We've finally pinned down why, which is too tedious to explain, but I don't like the mechanism anyway, as I have to give wordpress my username/password (for the command line, not for wordpress). So, I'm trying another solution. Check the whole thing out of SVN. I've just moved over to this me…

Emma in the Park

I've been meaning to go and see one of the outdoor performances in Jesmond Dene for a while. Last week, I finally got to one --- Emma, by Jane Austen, on a lovely, bright friday evening. The story itself isn't really up to much. Almost all of the main characters are unlikeable and unengaging; Emma, herself, is an interfering, arrogant and affected snob, with no redeeming characteristics; she barely stands out against the characters who are meant to be unpleasant. Very little happens that is of particular interest; I can't find it in my heart to be excited about a ball or a picnic. There wasn't even the consolation of a few tragic deaths; the one funeral is a minor character, and you can't take pleasure in that. During the big finale it all ends well for Emma who gets hitched; but, I felt s…

Planes, Trains and Boats

On Saturday, Newcastle was host to an Americana festival; anything with lots of music anywhere is always going to make me happy. In this case, we ended up a music boat; there's a company that regularly cruises up and down the Tyne, and I've long thought it might be fun to give this a go; what better than to combine this with a bluegrass band (the midnight ramblers) and Devon Sproule, who is always good to see. It was a good fun; the cruise itself was entertaining, especially with the weather being so nice. Unfortunately, you couldn't hear the band from the top deck, but as I'd forgotten my floppy hat, staying atop wasn't an option anyway. The band were fun; very competant, professional and fluid. Poking around their website, they appear to be part-time, which belies their touring schedule;…

New Categories

Following my holiday, I've decided to create two new categories for my blog, one for all my professional pieces and one for my personal. This blog fulfils two many purposes. Firstly, it serves as a memory aid for myself; I can look back at the things and the ideas that I've had in the past. Secondly, I use it to publish these ideas. I'm aware that the former is the more important than the latter; like most blogs, this site is not heavy traffic. I do publish about my personal life here, but this is not a full disclosure blog; it's called "an Exercise in Irrelevance" for exactly this reason. I put occasional reviews of things up; places I've visited or music that I've listened to. All about my reactions to public events. This blog isn't meant to be a soap opera. I also publish post…