Archive for November, 2007


I have been scooped on my own work! Deepak has managed to beat me in blogging about myspoon own screencast on the CARMEN project! Seriously though, thanks to Deepak for mentioning the project. I will have to blog harder and faster. As he highlights there are some challenges that the project hopes to address. Apart from the sheer demand for diskspace, one of the major challenges is to provide metadata to describe not only what an item of data is on the system but also how it was generated in the lab. In addition to this we also need a provenance trail describing what has been done on this data such as describing types of analysis to the degree of who authored the code, which version was it, where was it run and so on.

For the lab generation metadata we are trying to bring what we have learnt from within the biology/bionformatics community and take it a step further. We are currently assessing if the FuGE data model can be applied to electrophysiology . This may be achieved by creating an appropriate CARMEN ontology which we intend to align with OBI. It would be interesting to know if this seems like a sensible approach and of any alternatives we could employ.

The screencast of some introductory slides about the project and a demo of the current functionality of the CARMEN system can be viewed via the following screencast, hosted on Bioscreencast. I site I like and one which I begining to use more often.

I can seem to get it to embedd with wordpress so here is the link.



Latest bio::blogs

The 16th edition of Bio::blogs has been released on Freelancing Science. I enjoy reading Bio::blogs for two reasons:

  1. If I know it all already then I have been doing a relatively good job of keeping up to date with what has been talked about and I can convince myself that my knowledge is on the cutting edge of science ( this is rarely the case though)
  2. I always find a new blog or a new post that is interesting.

This month I noticed a screencast by Konrad  on open science and transparency which I though I would download to watch on my travels to San Diego. When I got there however I realized I had already seen it via Nature Precedings. Oh well must be on the cutting edge 🙂

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