Monthly Archives: July 2007

Lets Open up Science NOW!- letter from 26 nobel laureates to the US Congress

The letter  dated July 13 2007 , signed by 26 nobel laurates starts thus.
As scientists and Nobel laureates, we are writing to express our strong
support for the House and Senate Appropriations Committees’ recent
directives to the NIH to enact a mandatory policy that allows public
access to published reports of work supported by the agency. We believe
that the time is now for Congress to enact this enlightened policy to
ensure that the results of research conducted by NIH can be more
readily accessed, shared and built upon ­ to maximize the return on our
collective investment in science and to further the public good"

Read the entire letter here. But here are the key points
The signatories object to barriers that "hinder , delay or block the spead of knowledge supported by federal tax dollars"

A large amount of research continues to be inaccessible

The Voluntary policy
( requiring a submission to PubMed Central) has not worked. Its time to make it mandatory!

Several counties already do this and despite making this mandatory science has not suffered.

And finally

"Journals will continue to be the hallmark of achievement in scientific research, and we will depend on them."

Saw this first on Savas Parasatidis’s blog .

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Back on the NCBI horse

I have been working a lot with alignments in Jalview and had blogged about how Google can find Uniprot IDs better than NCBI ..well it turns out that NCBI did indeed have most of the Uniprot sequences I was looking for. The fault was mine! for not using the correct form of uniprot id..

The catch
I had to say just Q57T52 instead of the Q57T52_SALCH and Q325Y4 instead of Q325Y4_SHIBS

Which brings to me to one incredible thing about google. The google suggest and spelling correction. NCBI recently added the spelling correction feature. But still does not have something that would have told me that I should try Q57T52 instead of the old style Q57T52_SALCH uniprot id query.

So all in all out of the 742 sequences that the manually curated PFAM database had used in its voltage_clc gamily alignment. I could find almost 640 of them at the NCBI using the NCBI web service. All it took was understanding the existence of the deprecated uniprot id.

When I similarly tested the EBI web service for the same 742 sequences, only 582 sequences were obtainable in the uniprotxml format from the uniprotkb database.

As a final try , looking for some of the sequences that were missing in the better performing NCBI database , by doing a google search returned a match in the first few results. So google still is quite amazing in its ability to index even probably poorly page-ranked words like Q40LF7_DESAC. Surely the day they take on bioinformatics in a formal way will be a fun day to look forward to.

references : bbgm on a Google for Bioinformatics

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Exciting times on the science web : Timo Hannay on Nascent

I was very excited to read Timo Hannays post on the Nature Nascent blog where he reproduced an excerpt from his post for STM news on “how Oreilly and the alpha-geek crowd have influenced Nature Magazine”. Titled , web opportunity , the post talks about the great opportunities that lie in the web for all of science and science publishing.

In the very interesting post Timo talks about the democratization of audio and video and Natures experiments with the Nature podcast. The Nature podcast apparently started off as just an experiment and then grew to almost 30,000 downloads at the end of its first year.
The article talks about scientists who listen to the podcast when they are on the microscope and commuting in or exercising. In my own case, I find that thanks to the nature podcast I am now even more inclined to pick up my print copy, to follow up on something exciting I heard on the nature podcast.

Apart from the ability of audio and video to organize and nucleate communities, Timo also talks about Databases as being the conduits that enable collaborations and the role that publishers have in building communities . Towards this Natures several Gateways , are database driven community resources that aggregate content from both the community and NPG journals in several areas.

The article makes good reading and I will not paraphrase it any further

If I were to rank the web offerings from Nature in terms of their value to my current scientific life..my ranking would go thus
1) The Nature podcast
2) Connotea
3) The Nature Omics gateway

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