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;
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’ve been mulling over this for a while, and seeing as I am home sick (can’t you tell from the rush of posts?) I’m going to give it a go. This definitely comes with a health warning as it goes way beyond what I know much about at any technical level. This is therefore handwaving of the highest order. But I haven’t come across anyone else floating the same ideas so I will have a shot at explaning my thoughts.
During the workshop in late February we had discussions about possible implementations of Taverna work flows to automate specific processes to make our life easier. One specific example we discussed was the reduction and initial analysis of Small Angle Neutrons Scattering data. Here I want to describe a bit of the background to what this is and what we might do to kick of the discussion.
What Shirley said: The call for participation for the Open Science workshop at PSB 2009 is now up! We welcome anyone with an interest in open science to submit proposals for talks. Note that although space is limited for talks and demos, anyone who registers for the conference can present a poster, so we also encourage poster submissions! Please if you are interested in submitting a talk or poster get in touch.
‘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.
Shirley has already posted a quick notice on this but I thought I would follow up. Our proposal for a session at the Pacific Symposium on Biocomputing on Open Science was successful and we have been asked to put together a workshop session to run on January 5 next year in Hawaii. This is a slight departure for PSB. The workshop sessions are slightly shorter than the traditional sessions and full papers will not feature in the proceedings.
Another post prompted by an exchange of comments on Neil Saunder’s blog. The discussion here started about the somewhat arbitrary nature of what does and does not get counted as ‘worthy contributions’ in the research community.
More followup on feeds. I’ve set up a friendfeed which is available here. Amongst other things I’ve been trying to aggregate my comments on other people’s blogs. The way I am doing this is creating a tag in Google Reader which I have made public. When I leave a comment I try to subscribe to a comment feed for that Blog, I then tag it as ‘Comments feed’ which aggregates and makes it public as an RSS feed.
Following on from (but unrelated to) my post last week about feed tools we have two posts, one from Deepak Singh, and one from Neil Saunders, both talking about ‘friend feeds’ or ‘lifestreams’. The idea here is of aggregating all the content you are generating (or is being generated about you?) into one place. There are a couple of these about but the main ones seem to be Friendfeed and Profiliac.