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…