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First Wikipedia edit

I have just made my first edit in Wikipedia. The page in question described what now is the proliferation of life science reporting recommendations and can be found here. I added the details for the MIAPE GE recommendations and intend to add the neuroscience recommendations that I have been working on shortly.

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Updating blog roll

In an effort of catching up with the blog posts form 2007 before starting the ones for 2008, I have just gone through my Google reader subscriptions. As a result I though I would update my blogroll  accordingly with the blogs have have enjoyed reading over the last year. The list is over on the right but the new additions are bio::blogs; the monthly bioinformatics blog carnival, bioinformatics zen from Michael Barton, the CARMEN project blog (which I contribute to), Hugo Hiden, the technical director of the e-science institute here in Newcastle, Public Rambling by Pedro, Savas Parastatidis personal blog and What you’re doing is rather desperate

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FuGE users workshop

Fuge logo

I am at the FuGE users workshop at the moment which is being held in Manchester. The idea behind the workshop is that people who have used FuGE or extended FuGE for a specific use get together and share their experiences. I have used FuGE to develop GelML for the Proteomics Standards Initiative. GelML is one specification produced by the Gel-working group of the PSI, which is a data model to capture the use of gel electrophoresis in a proteomics experiment – but in theory it should be able to account for the use of gel electrophoresis independent of the use or domain. I presented GelML on the first day along with some discussion points I would like to see addressed over the two days. We have a small be varied set of users at the workshop covering the domains of flow cytometry, RNAi, proteomics and systems biology along with tool developers (Symba).

As the result of the workshop we hope to produce a set of recommendations or best practice guidelines to promote uptake and consistency of the use of FuGE, all of which is an honourable goal. In regard to this one interesting discussion was to provide a library or a set of desing templates for common constructs, such as instrument settings or the protocol to create buffers and solutions.

The workshop has been very productive so far and it has been very interesting to see how other domains have extended FuGE

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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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I am currently at the All Hands meeting 2007 in Nottingham, so more posts to follow with some notes on the events and presentations. In addition, a couple of people from my lab are also at the Integrative Bioinformatics conference in Ghent Belgium so you can follow Allyson’s and Matt’s comments on that event.

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I see science

It is interesting to see new developments in the dissemination of scientific discourse, such as scientific blogging and paradigms such as open science, come on-line with developments in web-based social media. The latest medium to receive the Science 2.0 treatment (poor pun on applying Web 2.0 technologies for science) is the video.

YouTube is probably the granddaddy, or at least the most prominent of the video upload and broadcast services. Although YouTube doesn’t not have a defined science category, it is easy to find science related videos and lectures, mixed in with the general population. However, several specialist sites have appeared dealing specifically with science research, all have been labeled as “YouTube for science”. The most recent site is SciVee, which is a collaboration of the Public Library of Science (PLoS), the National Science Foundation (NSF) and the San Diego Supercomputer Center (SDSC). The fact the a publishing house (PLoS) has got involved in this effort is encouraging, and maybe an admittance that a paper, in isolation of public commentary, the data used to produce the paper, and a sensible presentation mechanism, is no longer sufficient in the web-based publishing era (or maybe I have got over excited and read to much into it). The most interesting feature on SciVee, and probably the most powerful compared to some of the other broadcasters, is the ability to link to an Open Access publication, setting the context and relevance of the video. The flip side could also be true, where a video provides evidence of the experiment, such as the methods or the displays the result.

Another scientific video broadcaster is the Journal of Visualized Experiments (JOVE). As the name suggests, JOVE focuses on capturing the experiment performed within the laboratory, rather than a presentation, or general scientific discourse. As a result JOVE can be though of as a visual protocol or methods journal and is stylaised as a traditional journal, already on Issue 6; a focus on Neuroscience.

If JOVE is a visual journal for life-science experiments then Bioscreencast could be thought of as a visual journal of Bioinformatics. Bioscreencast focusses on screencasts of software, providing a visual “How-to” on scientific software, presentations and demonstrations.

No doubt these three may not be the last scientific video publishers, but they have an opportunity to become well established ahead of the others. Now, where is my webcam, I need to video myself writing code and submit it to JOVE, produce a demo and submit it to Bioscreencast. Then I have to write a paper on it, submit the pre-prints to Nature Preccedings get it published in an Open Access Journal, then video myself giving a presentation on the paper, submit it to SciVee and link them all together.



There is lots of blogging activity at the minute around Scifoo. I am excited, just reading the posts and looking at the range of people there, not to mention the range topics on discussion. The most comprehensive one I have found is Duncan’s on Nodalpoint, and bbgm although there are other people which you can probably track via the scifoo Technorati tag

I wish I was there, oh well maybe next year……….

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No more session restore in Firefox

I continually get greeted with the “restore last session” pop-up when I start firefox. I find it really annoying especially as I use Google Browser sync to do exactly the same thing, so I have to deal with two restore messages.  I have followed the following link and turned off the session restore feature in firefox.

1. type about:config in your browser URL
2. go to the browser.sessionstore.enabled setting
3. change the setting to false


Ontology of Scientific Experiments

NewScientist of all places are talking about ontologies. Specifically An ontology for scientific experiments.

"Called EXPO, it can be used to translate scientific experiments into a format that can be interpreted by a computer."

Wow! translate experiments, that's impressive I would love to find out how the scrawny hand-writing, contained inside the standard lab notebook, dog-eared and drenched in all manner or reagents, gets translated into an ontology, that's more impressive than the ontology itself.

However on a more serious note, I agree with the concept, that something like this should exist. It would definately help in dissemination and analysis of data (providing the data is freely provided and in a standard structure of format), but this kind of process, an ontology for all of science, would have to have a major open development across all scientific disciplines, as FUGO (Functional Genomics Investigation Ontology) are doing, in order to be agreed upon and for the claim that it represents all scientific experiments.

Going by the article, and snooping around the EXPO site, a cross discipline development process doesn't appear to have taken place, or planned for the future (my apologies if this is not the case). And according to the article it has been tested on two use-cases, one on particle physics and one on evolutionary biology, this must be the only wet-lab science that exists these days. It would be interesting to see if the large scale collaboration effort of FUGO agrees with or already has a similar structure to EXPO
A quote at the bottom of the article says "Software to speed up this process could be a big boost ", I think he meant to say, "This would be impossible without software being available from the wet-lab bench, to data storage, to the publication process".

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