…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’m in Barcelona at a satellite meeting of the EuroScience Open Forum organised by Science Commons and a number of their partners.  Today is when most of the meeting will be with forums on ‘Open Access Today’, ‘Moving OA to the Scientific Enterprise:Data, materials, software’, ‘Open access in the the knowledge network’, and ‘Open society, open science: Principle and lessons from OA’. There is also a keynote from Carlos Morais-Pires of the European Commission and the lineup for the panels is very impressive.
Last night was an introduction and social kickoff …

As has been noted in a few places, Neil Withers, one of the editors of soon to be newest Nature journal, Nature Chemistry put out a request last week for input on a range of issues to do with how people use journals, formats, and technical widgets. Egon Willighagen, Rich Apodaca, and Oscar the Journal Munching Robot (masquerading as Peter Murray-Rust, or is that the other way around?) have already posted responses. Here I want to add my own thoughts and possibly amplify some of the points others have made.

Image from Wikipedia via Zemanta
Following on from the discussion a few weeks back kicked off by Shirley at One Big Lab and continued here I’ve been thinking about how to actually turn what was a throwaway comment into reality:
What is being generated here is new science, and science isn’t paid for per se. The resources that generate science are supported by governments, charities, and industry but the actual production of science is not supported. The truly radical approach to this would be to turn the system on its head. Don’t …

Frank Gibson has posted again in our ongoing conversation about using FUGE as a data model for laboratory notebooks. We have also been discussing things by email and I think we are both agreed that we need to see what actually doing this would look like. Frank is looking at putting some of my experiments into a FUGE framework and we will see how that looks. I think that will be the point where we can really make some progress. However here I wanted to pick up on …

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 …

As I mentioned a couple of weeks or so ago I’ve been playing around with Friendfeed. This is a ‘lifestreaming’ web service which allows you to aggregate ‘all’ of the content you are generating on the web into one place (see here for mine). This is interesting from my perspective because it maps well onto our ideas about generating multiple data streams from a research lab. This raw data then needs to be pulled together and turned into some sort of narrative description of what happened.

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 …

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 …