In previous posts I have discussed the setup and rationale for how we are organising our blog-based electronic laboratory notebook. This has covered how the blog is actually organised. In this post I will look at the issue of how we actually view the blog and extract information. The organisation of the blog with a ‘one item one post’ approach creates a problem. There are a large number of posts to describe even a relatively simple process.

I am continuing this in a new post rather than keeping mucking with the old one. Currently I am working on reproducing the description of Exp098 from Jean-Claude Bradley’s UsefulChem Wiki within our blog based notebook to identify differences in practise.

In a previous post I said I would try to replicate an experiment from the UsefulChem open Wiki notebook within our blog system to see how it might look. This post is to record what I am doing as I do it. Thus this is the lab book I am using to record the process and decisions I have taken in using a lab book.

Well when it’s not open obviously. There are many ways to provide all the information imagineable while still keeping things hidden. Or at least difficult to figure out or to find. The slogan ‘No insider information’ is useful because it provides a good benchmark to work towards. It is perhaps an ideal to attain rather than a practical target but thinking about what we know but is not clear from the blog notebook has a number of useful results.

I wanted to pull out some of the comments Jean-Claude Bradley has made on the e-notebook posts and think them through in more detail. Thinking about this and looking at some examples on the UsefulChem Wiki I wondered whether this is largely down to a different way of thinking about the notebook rather than differences in field. I will use the UsefulChem Exp098 as an example for this.

I wanted to followup on the post I wrote a few days ago where I quoted a post from Black Knight on the concept of making methodology open. The point I wanted to make was the scientists in general might be even more protective of their methodology than they are of their data. However I realised afterwards that I may have given the impression that I thought BK was being less open than he ‘should’, which was not my intention.

Continuing the discussion set off by Black Knight and continued here and by Peter Murray-Rust I was interested in the following comment in Black Knight’s followup post (my emphasis and I have quoted slightly out of context to make my point). A lot of the debate has been about posting results and the risk of someone stealing them or otherwise using them. But in bioscience the competitive advantage that a laboratory has can lie in the methods.

I wrote the other day about the idea of fun being a motivating factor to taking up open notebook science. Sometimes something is just cool and you want to share it. Then along comes a great example. Via petermr’s blog: At ‘Life of a Lab Rat’: As petermr says this is just very cool. The molecular biology is fairly conventional. But that’s not the point.

The reasons for pursuing more openess in science from the perspective of the science and funding communities have been well rehearsed and described elsewhere (see 3 Quarks Daily 1,2, and 3 for an excellent overview). There are excellent discussions of where this might take us in terms of capability and in terms of the efficient re-use of government or charity funded research.

Open [oh-puhn ] (adjective) not closed…having no means of closing or barring…relatively free of obstruction…without restrictions as to who may participate…undecided; unsettled… (from Dictionary.com) There is a great deal of confusion out there as to what ‘Open’ means, especially in science. The definitions above seem particularly apposite ‘…relatively free of obstruction…’. Certainly undecided or unsettled seems appropriate in some cases.