This is the second of two posts discussing the talk I gave at the Science 2.0 Symposium organized by Greg Wilson in Toronto in July. As I described in the last post Jon Udell pulled out the two key points from my talk and tweeted them. The first suggested some ideas about what the limiting unit of science, or rather science communication, might be. The second takes me in to rather more controversial areas:
@cameronneylon uses tags to classify records in a bio lab wiki. When emergent ontology doesn’t match the …

Just a brief thought prompted by two, partly related, things streaming past my nose. Firstly Michael Nielsen discussed the views of Aristotle and Sunstein on collective intelligence. The thing that caught my attention was the idea that deliberation can make can make group functioning worse, leading to a collective decision that is muddled rather than actually identifying the best answer presented by members of the community. The exception to this is well posed questions, where deliberation can help. In science we are familiar with the idea that getting the question …

The second installment of the paper (first part here) where I discuss building tools for Open (or indeed any) Science.
Tools for open science – building around the needs of scientists
It is the rapid expansion and development of tools that are loosely categorised under the banner of ‘Web2.0’ or ‘Read-write web’ that makes the sharing of research material available. Many of the generic tools, particularly those that provide general document authoring capabilities, have been adopted and used by a wide range of researchers. Online office tools can enable collaborative development of …

Something that has been bothering me for quite some time fell into place for me in the last few weeks. I had always been slightly confused by my reaction to the fact that on UsefulChem Jean-Claude actively works to improve and polish the description of the experiments on the wiki. Indeed this is one of the reasons he uses a wiki as the process of making modifications to posts on blogs is generally less convenient and in most cases there isn’t a robust record of the different versions. I have …

…is knowing what you mean…
I posted last week about the spontaneous CMLReact hackfest held around Peter Murray-Rust’s dining room table the day after Science Blogging in London. There were a number of interesting things that came out of the exercise for me. The first was that it would be relatively easy to design a moderately strict, but pretty standard, description format for a synthetic chemistry lab notebook that could be automatically scraped into CMLReact.
Automatic conversions from lab book to machine readable XML
CMLReact files have (roughly) three sections. In …

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 …