Home » Archive

Articles tagged with: e-notebook

Blog »

[2 Oct 2007 | Comments Off on Joint NSF-EPSRC programme in Chemistry – an opportunity for ONS? | ]

Looking at the EPSRC website I came across the following call for proposals involving collaboration between a US and UK programme:
http://www.epsrc.ac.uk/CallsForProposals/NSF-EPSRCChemistryProposals07.htm
Now, being an academic I’m up for any method of trying to get money out the system, especially special programmes. But is there an opportunity here to do something quite exciting in the area of Open Notebooks for chemistry where we take Jean-Claude’s experience and our Lab Blogbook system and try to build something that combines the best of both or possibly better, something which is a superset of both? …

Blog »

[25 Sep 2007 | 7 Comments | ]

Yesterday afternoon the Open Notebook Science case studies session was held as part of the Scifoo lives on sessions at Nature Island, Second Life. Jean-Claude Bradley organised, moderated and spoke first followed by me and Jeremiah Faith. We all spoke about experiences and implementation of different approaches to open notebook science.
Jean-Claude has put the transcript up here.
There was an active discussion about the need for more fun in science and the way in which science has become secretive has taken a lot of the fun out of it. CW Underwood …

Blog »

[21 Sep 2007 | 14 Comments | ]

Research in most places today is done under more or less rigorous safety regimes. A general approach which I believe is fairly universal is that any action should in principle be ‘Risk Assessed’. For many everyday procedures such an assessment may not need to be written down but it is general practise in the UK that there needs to be a paper trail that demonstrates that such risk assessments are carried out. In practise this means that there is generally for any given laboratory procedure a document of some form in …

Blog »

[20 Sep 2007 | Comments Off on The Southampton Electronic Blog Notebook – Part 4 – Visualisation | ]

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. For instance running two PCR reactions involves at least three posts, even before there …

Blog »

[18 Sep 2007 | 4 Comments | ]

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. The reproduction can be found at;
http://chemtools.chem.soton.ac.uk/projects/blog/blogs.php/blog_id/15/
then click on ‘Usefulchem_exp098′ under the ‘Sandpit Group’ heading on the right hand side and explore from there
18/09/07 15:00 UTC I have added the next two steps of the experiment, the addition of methanol followed by the addition of NaOH to neutralise the solution. In …

Blog »

[13 Sep 2007 | Comments Off on Replication of UsefulChem Exp098 in the Southampton blog notebook | ]

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. The pages in the notebook can be found at;
http://chemtools.chem.soton.ac.uk/projects/blog/blogs.php/blog_id/15/
I have chosen to use Exp098 as this involved several different stages and modifications to the wiki …

Blog »

[10 Sep 2007 | One Comment | ]

If it hasn’t been obvious from what has gone previously I am fairly new to the whole E-science world. I am definitely not in any form a computer scientists. I’m not a computer-phobe either but my skills are pretty limited. It’s therefore a little daunting to be going for the first time to an e-science meeting. This is the usual story of not really knowing the people from this community and not necessarily having a clear idea of what people within the field or community think the priorities are.
The programme …

Blog »

[3 Sep 2007 | 12 Comments | ]

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. Clearly it helps us to see how open we are being but …

Blog »

[27 Aug 2007 | Comments Off on Southampton blog notebook at UK All Hands E-science meeting | ]

Just a short note to say we will be doing a demonstration of the blog notebook at the UK E-science All Hands meeting being held in Nottingham in a few weeks time. We will be on the BBSRC stall at 13:40 on Wednesday 12th September assuming everyone else runs to schedule. If you are at the meeting do drop in and say hello.

Blog »

[23 Aug 2007 | 4 Comments | ]

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.
Jean-Claude‘s comment on this post:
There may be differences between fields but, in organic chemistry, we could not make a blog by itself work as an electronic notebook. The key problem was the assumption that an experiment could be recorded without further modification. But a lab notebook doesn’t work like that – the idea is to record work as it is being done and make observations and conclusions …