A new way of looking at science?
I’ve spent a long time talking about two things that our LaBLog enables, or rather that it should enable. One is that by changing the way we view the record we can look at our results and materials in a new way. The second is that we want to enable a machine to read the lab book. Andrew Milsted, the main developer of the LaBLog and a PhD student in Jeremy Frey’s group, has just enabled a significant step in that direction. He’s managed to dump my lab book as rdf which enables us to look at it in an rdf viewer such as Welkin, developed by the Simile group at MIT.
At the moment this just shows each post as a node and the links between posts as edges. But there a number of things that are immediately obvious. The first is that I start a lot of things and don’t necessarily manage to get very far with them and that I do a number of (currently) unrelated things (isolated subgraphs aren’t connected). Also that there are some materials that get widely re-used and some that don’t. There are also clearly things that I haven’t finished entering properly (isolated nodes). Finally, that we need a more sophisticated tool for playing with the view because building a human readable version of the graph will require some manipulation, grabbing subgraphs and moving them around. Welkin is great but after 30 minutes playing I have a bunch of feature requests. But this is what I’ve done so far. I am sure there are many things that can be done with this kind of view – but for the moment what is important is that it is an entirely new kind of way of looking at the record.
For those interested in following progress on another story, the data and analysis built on the model that Pawel Szczesny built for us is in the bottom right hand corner of the graph. You can see thatat the moment it is isolated from the rest of the graph because we haven’t yet compared these models with our experimental results (actually the relevant experiments aren’t on this graph because it was dumped before we did them). That’s something we should be doing in the next few days. If the data matches the model (current indications are that it does, but data quality is an issue) then we will have something very interesting to say about the structural changes on ligand binding in ligand gated ion channels.