Category Archives: open access

Of $6 web hosts and dying web apps

Just yesterday I was reading tiagos blog where he requested hosting for a computational intensive bioinformatics web-app that he wrote. The application queries and sytematizes mitochondrial genome information from entrez databases, and I assume would be quite useful to animal geneticists and ecologists. Tiago is physically moving institutes and his blog posts talks of his fears of how the app might die if his personal computer goes down.

In one of my personal projects , I have been wrestling with cloning kappa light chains from several monoclonal antibodies that I generated. The cloning required a good knowledge of the anitbody light and heavy chain leader sequences . Several papers I was reading reference the Kabat and Wu database, which catalogs the thousands of sequences of antibodies and other immunological proteins from mouse and humans . Sadly the links to the Kabat and Wu database in some of these papers does not point to any meaningful location. The resulting google and pubmed searches to find this lost data greatly increased the time and effort required to design my cloning experiments.

Which brings me to my question.

In an era when we have free wiki hosting , 4 GB free email access , supercomputers that power maps , gigabyte large free image sharing applications, $6 per month, terabyte bandwidth web hosting. Why are we still so far from an advertisement supported “free” app host for meaningful scientific data ?

Perhaps its because only a few thousand people who are saving a rare turtle species somewhere on this planet will find tiagos web-app useful..Surely thats not yet worth enterprise level attention, or maybe we should all just write our web apps to run off facebook!

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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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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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Nature precedings : A great offerring from the NPG stable

Nature just launched Nature precedings , a home for Pre-publication research and preliminary findings. Within seconds of browsing through its very intuitive interface I immediately got the purpose of this offering from Nature Publishing group.

The way it works is simple- you can upload content in the form of word documents , powerpoint files and pdf files and it gets released to the community after a preliminary check for appropriateness of content and suitability for the nature precedings audience. Signed up users can then vote on the content ( a la Digg) and it gets moves up or down its category. All of the content is also search-able and link-able and citeable.

As the help pages suggest, I hope the site serves , in the least as a repository of supplementary material and science findings related to published work anywhere, which can then be commented on and discussed.

More interestingly the FAQ page, informs us that the Nature publishing group Journals do accept material that is in the un-peer-reviewed form and that has appeared in the preprint form : So if i get together a manuscript , I can first post it on Nature precedings and then send it for consideration to Nature for review separately and nature would still consider it ( if it meets its other criteria of course).

So this site could be a great place to establish the provenance of ideas, i.e I have a great new finding , I am gutsy enough to write it up in some form , post it on Nature precedings ..and then a few months later send the finished work to a print journal like a Nature publishing group journal that would accept it.

With all of this Nature precedings has the great potential to become an online repository of pre-print findings , supplementary material and other content of use to the science community…I really cant wait for the first paper to make it from Nature Precedings to the real thing , Nature itself with a citation that first appeared online!.

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University-knowledge beyond authority

Knowledge Beyond Authority at Harvard Law SchoolI have recently started attending the Berkman Centre Thursday Blog group meetings. The meetings which are open to the general public were started many years ago by Dave Winer and colleagues and are loosely structured to discuss topics related to blogging, the social web and also recently ( since I have been attending) entrepreneurial activity in the web 2.0 space from local startups .

At the meeting I heard from Mike Walsh of a conference to be organized by the center titled , University- knowledge beyond authority.
The conference aims to “generate questions, insight and solutions from diverse perspectives across the landscape of University, with a focus on the role of University as an institution.We seek to establish University as a collective force much like ‘Government’ or ‘Private Enterprise’ in its ability to negotiate and compromise for our needs in the digital environment.”

The conference has several sessions dealing with topics ranging from fair use , open-access to discussing the relationships between “University” and library and the RIAA.

The concept of University it seems is to organize thought and opinion on these topics from an educational perspective. Since I know very little about the complex world of licensing , and the DMCA is almost a four letter word to me, it will be fun to listen to how this concept of University evolves at University.

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