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 …
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…
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
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.
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
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 …
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
was very helpful, although their technique doesn't completely work. I…
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…
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.
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
I've just moved over to this me…
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
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
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…