Archive for January, 2008

Standard Open(ed-up) Science

Posted by peanutbutter in bioinformatics, data standards, open data, open science, Proteomics, Thesis on January 28, 2008

OK, so it is not quite up to the minute as-you-do-it-you-publish-it open science. However, I plan to make my data that I generated during my PhD (just finished) open and available, and in writing this post I am making some what of a public commitment to do so. Once difference though, from some of the open science efforts that I have seen so far, is that I will be publishing my data, conforming to the Proteomics Standards Initiative(PSI) MIAPE guidelines for gel electrophoresis (MIAPE GE.pdf) recommended reporting requirements. The data itself will be represented in XML using the PSI recommended gel electrophoresis Mark up Language (GelML), and using terminology from sepCV and OBI should mean the data set is computationally amenable. I was involved in the development of these specifications so I suppose I should be leading by example and be the first one to publish a complete gel electrophoresis proteomics dataset.

When finnished, I would have liked it to be published some where like Nature Preceedings, however they only accept proprietary Microsoft files and pdfs rather than XML documents. I also though of creating a Google code project for it, but it seems quite elaborate for something nobody else would be contributing to and once completed would be rather static. Any suggestions are very welcome.

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First Wikipedia edit

Posted by peanutbutter in Uncategorized on January 7, 2008

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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goPubmed

Posted by peanutbutter in bioinformatics, Journals Publishing, ontology, search, semantic web, Social Media on January 6, 2008

In catching up with my reading lists of 2007 I was alerted to gopubmed via Deepak’s post. Gopubmed described itself as an ontology based literature search making use of both the Gene ontology and Mesh terms. There is also the ability to provide feedback or rather act as a curator for the search results. I have already noticed  some mis-match in author details.  In general though the interface  is a vast improvement on pubmed’s tiered interface and the ability to refine the searches looks interesting. I have added gopubmed to  my search engines within firefox and will have a play to see if it is any good. RSS feeds on search terms would be top of the wish list. Anybody used it in anger?

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Updating blog roll

Posted by peanutbutter in Uncategorized on January 6, 2008

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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