In the first post in this series I identified a series of challenges in scholarly publishing while stepping through some of the processes that publishers undertake in the management of articles. A particular theme was the challenge of managing a heterogenous stream of articles and their associated heterogeneous formats and problems, in particular at a large scale. An immediate reaction many people have is that there must be technical solutions to many of these problems. In this post I will briefly outline some of the charateristics of possible solutions and …

I spent today at an interesting meeting at Talis headquarters where there was a wide range of talks. Most of the talks were liveblogged by Andy Powell and also by Owen Stephens (who has written a much more comprehensive summary of Andy’s talk) and there will no doubt be some slides and video available on the web in future. The programme is also available. Here I want to focus on Andy Powell’s talk (slides), partly because he obviously didn’t liveblog it but primarily because it crystallised for me many aspects …

And other big words I learnt from mathematicians…
The observant amongst you will have realised that the title of my previous post pushing a boat out into the area of semantics and RDF implied there was more to come. Those of you who followed the reaction [comments in original post, 1, 2, 3] will also be aware that there are much smarter and more knowledgeable people out there thinking about these problems. Nonetheless, in the spirit of thinking aloud I want to explore these ideas a little further because they underpin …

Frank Gibson has continued the discussion that kicked off here and has continued here [1, 2, 3, 4] and in other places [1, 2] along the way. Frank’s exposition on using FuGE as a data model is very clear in what it says and does not say and some of his questions have revealed sloppiness in the way I originally described what I was trying to do. Here I will respond to his responses and try to clarify what it is that I want, and what I want it to …

This started out as a comment on Peter Murray-Rust’s response to my post and grew to the point where it seemed to warrant its own post. We need a better medium (or perhaps a semantic markup framework for Blogs?) in which to capture discussions like this, but that’s a problem for another day…

More on the discussion of structured vs unstructured experiment descriptions. Frank has put up a description of the Minimal Information about a Neuroscience Investigation standard at Nature Precedings which comes out of the CARMEN project. Neil Saunder’s has also made some comments on the resistance amongst the lab monkeys to think about structure. Lots of good points here. I wanted to pick out a couple in particular;
From Neil;
My take on the problem is that biologists spend a lot of time generating, analysing and presenting data, but they don’t spend much …

Frank Gibson of peanutbutter has left a long comment on my post about data models for lab notebooks which I wanted to respond to in detail. We have also had some email exchanges. This is essentially an incarnation of the heavyweight vs lightweight debate when it comes to tools and systems for description of experiments. I think this is a very important issue and that it is also subject to some misunderstandings about what we and others are trying to do. In particular I think we need to draw a …

‘No data model survives contact with reality’ – Me, Cosener’s House Workshop 29 February 2008
This flippant comment was in response to (I think) Paolo Missier asking me ‘what the data model is’ for our experiments. We were talking about how we might automate various parts of the blog system but the point I was making was that we can’t have a data model with any degree of specificity because we very quickly find the situation where they don’t fit. However, having spent some time thinking about machine readability and the …

This morning I got to sit down with Bill Flanagan, Barry Canton, Austin Che, and Jason Kelly and throw some ideas around about electronic notebooks. This is an approximate summary of some of the points that came out of this. This may be a bit of brain dump so I might re-edit later.

Neither Wikis nor Blogs provide all the functionality required. Wikis are good at providing a framework that within which to organise information where as blogs are good at logging information and providing it in a journal …

Given that most people reading this probably also read the UsefulChem Blog I would guess that they have already figured out I am visiting the States. However as I am now here and due to jet lag have a few hours to kill before breakfast I thougt I might detail the intinerary for anyone interested.