Last night was my first time at the Cluny 2, which used to be the Round,
as some of the signs inside still claim. It's not round any more, having
a conventional stage. There is still noise from the Cluny 1 upstairs and
the occasional flushing of toilets; I guess that they can't complain
about this anymore.
The support was Naomi Sommers. Pretty
standard format, really, one woman and a guitar. She has a lovely voice,
rich and warm which made the show. Some of her songs are pretty strong
("February"); some were less good, but no bad ones. Enjoyable.
Eric Taylor, I've not seen before. He also has a great voice, supported
by some excellent finger-picking. His stage presence is dark and
melodramatic. He's also a bit nuts; songs were separated by repetitious
and rambling talks about, we…
There is a mystery behind Brains SA; what exactly does it stand for?
Among those who know, it is universally revered as skull attack. I've
reasonably fond of it, but tonight, perhaps, I finally understood how it
came by it's moniker.
After getting home, following several pints, I was suddenly struck by a
desire to listen to Jimmy Sommerville; there is, of course, no sanity or
logic to this at all, but there you have it. Now, of course, his pop
sensibilities are well known, but I remember, like a folk memory hidden
deep in my brain, "For a friend" released shortly, perversely after
"Never Can Say Goodbye". No dancy pop tune this, but an elegiac ballad
to a friend lost to the virus of the 80s. I think I only heard it twice
before it disappeared; but I remember it was wond…
Beginning of term, so I guess it's not too much of a surprise that I
haven't blogged for ages. Life does get slightly swamped by work at this
time of year; yesterday, I was so tired after working at full-tilt for
two weeks that I even took most of the day off.
Anyway, I realised that I've been missing out on films that I have
watched, so I thought to do a quick, condensed review here. All of them
films that I've been looking forward to, but only 1 managed to fulfil
its promise.
So, Spiderman III. I do enjoy superhero films; plenty of action, add a
bit of pathos and some humour; then, you have a food film, especially
good for a plane or otherwise. Spiderman I and II were, I thought, great
examples. No III was one too far; basically, the plot was too winding,
too random; it just felt like a …
At Neuroinformatics 2009, David Sutherland and I talked about the
problems of ontology building. One of the current (and past!)
difficulties is to choose an appropriate language for representing the
knowledge in your ontology. I thought I would write my thoughts up as a
post; this will probably result in the most boring thing I have ever
written (I am sure someone will point out worse offenses); syntax is
dull but distressingly important.
In bioinformatics, there are essentially two choices that is OWL and OBO
(format). A second issue, is finding a good environment for developing
the ontology; this divides between Protege, OBO-Edit and the
ever-present "text editor". It's often the case, that we want to use
both of these at the same time. Take, for example, OBI, which I am
involv…
This is the third year in a row that I have been to Neuroinformatics (or
it's forerunner, Databasing the Brain). It's still turning out to be an
enjoyable meeting, even though there is still lots of it that I don't
understand. Come to think of, perhaps because there is lots of it that I
don't understand.
Pilsen (or Plzen) is, perhaps, a strange place for the meeting. It's a
bit of a pig to get to, as the airport is in Prague. Likewise, the
conference centre was a bit out of town, so you had to get a taxi if you
wanted food in the evening. Still the venue itself worked well. Slightly
flaky wireless, but it had tables upstairs on a balcony; a lot of people
migrated up there as the meeting went on, making the auditorium a little
deserted.
Although, I've said I didn't understand lots of it, ma…
Make has been driving me mad for the last
week. It keeps on complaining about "modification time in the future".
Normally, this happens because you're using rmeote files from a server
which doesn't have sync'd time. But this is rare these days. Anyway, it
was complain that the file was 10E+06 seconds in the future; that's a
really, really big clock skew.
Did a bit of poking around. One possibility I found was that it was due
to a limitation in FAT32; hmmm, not likely. Didn't have time for more. I
am at a conference; supposed to be paying some attention.
Anyway, the solution came to me today. Or rather the cause, because the
solution was obvious. Turns up, when I changed timezone to Czech, I
pushed the month back to August. What I don't understand is that I was
sure windows synced…
This is a live blog from Neuroinformatics 2009.
Data management: View from 50,000 feet --- dimensions are amount of
structure and the number of data sources. More structure, less data
sources.
Distinguishes between parallelisation and heterogeneity. Can distribute
data across tables in an organised way --- this is parallelisation; or,
you can have lots of data, spread across resources, with multiple
entities and with no common plan.
Outline --- data integration and suggest data spaces as a solution.
Databases are so successful because it provides a level of abstraction
over the data. Data integration is a higher level of abstraction still
because you don't have to worry how the data is stored or structured.
Mediated schema, uses a mediation language, a mapping tool, and then a
set of wrapp…
This is a live blog from Neuroinformatics 2009.
All of our observations about the brain are in some sense reductionist.
We are looking at only thing at a time, and hope to infer knowledge from
this. The knowledge is multi-technique --- no single experiment is going
to give the entire answer. Need to combine and integrate. Most of our
data is descriptive --- MRI is not that different from phrenology in one
sense.
Process of dissemination --- the web and equivalent --- has been
transformative of neurosciences. Large scale consortia are also
important; has been involved in lots of these --- sometimes
painful --- but useful. Good to learn the lessons from these.
The biggest lession from multisite brain mapping projects --- the data
needs to be open. If that data is open people will come, so lo…
Guiding principles of NIF. Builds heavily on existing technologies.
Information resources come in all sorts of size and shape.
Highest level NIF registry. Web index of resources which are relevant to
neurosciences.
NIF resource diversity --- three different levels of data, with
increasing amount of structure.
Is GRM1 in cerebral cortex? NIF system allows searching over multiple
different resources. But problems; inconsistent and sparse annotation of
scientific data. Many different names of the same thing and so on. Added
to this there are over 2000 databases in the registry.
Uses mixed searching so that both ontological information and string
based systems important for where there is no annotation. Can also do
query expansion with ontology to get better querying.
Building ontologies is di…
This is a live blog from Neuroinformatics 2009.
Motivation, what is the common feature of a set of disorders. They are
all complex disorders, which we don't really understand.
Alzforum is a nice example of an early web community. Alzheimers forum.
Works as an ongoing journal club, with curated discussions. Started off
during the early days of the web.
Developed StemBook which is an online book, launched about a year ago.
Discussion of stuff that is happening. pd online research, is another
alzheimers website, using a toolkit that they have developed. Linking
across these forums can be a problem; need some forms of shared
terminology server. Science Collaboration Framework. Based around
drupal, allows common collaborative tools for biomedicine, shared
ontologies/vocabulary and so on.
How do…