Saturday, December 15, 2012

FOAM, not what you think

Free Open Access Medical Education, who doesn't already love the concept, regardless of the number of hundreds of thousands of dollars "invested" into one's education?, #FOAMed (twitter, i guess)
As I've been only reading the emergency medicine blogs, i first stumbled across it there, but it seems to be a rapidly expanding movement promoted by the online leaders in the field (Scott Weingart, of EMCrit; Michelle Lin, of academiclifeinem).
I feel this is extremely pertinent to the Open Science Movement and wanted to keep everyone abreast of this new phenomenon!

Monday, October 1, 2012

One Scientist's Solution... the question of where do we get funding if not from institutions and grants, which provide such research money based on merit defined as publications, presentations, etc, is crowd-funding the fees.

A really neat article and video about Ethan Perlstein's approach to the open science and open source model and his research on evolutionary pharmacology.  This is a fantastic idea and could be used as a model for other researchers out there.  This at the very least could be used as a means for researchers to  engage open science and sharing data and cultivating a public collective conscience about scientific research and its funding.

Thursday, September 27, 2012

Greg Henry's "Renewing Research"

Some great commentary on working toward a smarter research culture: "Renewing Research," by Greg Henry.

Generally, he's reminding you to do the right thing because it's the right thing to do, whether you're doing research or running the free world. Huge appreciation of his liberal arts-style editorializing in the medical literature.

Here's a link.

For those involved with emergency medicine, there are a lot of strong, provocative articles linked from the parent website.

Wednesday, September 26, 2012

Spin in medical literature, a cohort study

Hey, all,

A cool little study published in PLoS Medicine linked here.

Essentially, it's a "retrospective cohort study" looking at factors influencing relative hyperbole, or "spin", that appears in the news media following the publication of new medical science (specifically, randomized controlled trials). The authors conclude that, most commonly, spin creeps into the news when study authors include it in press releases. Ultimately, it suggests both that press releases need to be done responsibly and that the news media rarely reads or digests our newly published scientific literature!

I'll admit that, when overloaded with things to read and process with limited time, I occasionally take the easy route, skip past my assessment of medical literature, and begin with the conclusions. I think we all do.

There's clearly a problem if we're expecting outsider-types to digest our literary canon to separate our trashes from our treasures. They don't have the background in epidemiology/biostatistics/whatever scientific field we're publishing from to do so. Ultimately, even if they did, it isn't in the press' interest to restrict hyperbole.

So it's agreed: responsible, accurate press releases from now on. Good.

Wednesday, September 5, 2012

Open Science Competition

This is a pretty awesome:  Genspace and Assay Depot are holding a competition in the tri-state area of NY, NJ, and Connecticut looking for the best amateur innovators and researchers with cash prizes for receiving top marks.  This article does an excellent job of describing all the basics behind it. 

What would be great is the ability to have a much wider dispersion of these sorts of competitions.  As much as anyone may like to tinker or experiment, having the incentive of cash to really throw some results to the greater public is a perfect theater for open science to grow.  These competitions also would provide an excellent means of getting these amateur scientists to meet and possibly collaborate, putting a face to to the facebook of open science, perhaps.

Sunday, August 26, 2012

Open Science Startups and Supercomputers

Seems like everyone is figuring out the shtick of open science can be a highly desired enterprise:  Mendeley, a London-based startup, acts as a Wikipedia of open science and has really exploded in terms of its monthly traffic.  Check out Mendeley's site here to learn more.

Not only that, more and more investments into collaborative science are being made with hefty investments.  The National Energy Research Scientific Computer Center (NERSC) signed a $40 million supercomputer agreement with Cray Cascade System with a specific aim of advancing open science efforts. 

So here we have examples of how there are very lucrative means of engaging open science as well as sites available to really get involved, not to mention innumerable other groups like Mendeley.  Seems like some things are going in a very positive direction.

Sunday, July 15, 2012

Open-Access UK

In an unprecedented move toward open-access, the British government unveils plans to make all tax-payer funded research available free to readers by 2014. Controversial? Yes. Necessary? Absolutely.

Read the complete article here.

Can we expect a similar transition in the US?

Call your congressman!

Monday, May 21, 2012

Sequestered Data Hinders Scientific Process

Apologies for the lengthy sabbatical, open science news has been abounds.  Recently large companies with monstrous data banks of (occasionally personal) information have been working with a select number of researchers to publish articles, but refuse to share such banks with other researchers for any verification or scrutiny.

"It’s antithetical to the basic norms of science to make claims that cannot be validated because the necessary data are proprietary." - Michael Eisen

Check out the article here.


Tuesday, April 24, 2012

Harvard slams the publishing industry racket

For those who haven't participated in scientific publishing directly, I'll describe it briefly:

A scientist, potentially funded by your tax dollars, has research he wants to publish. He writes a manuscript using data he's accumulated using this funding. That manuscript is submitted to a scientific journal (like Nature or JAMA) and undergoes a peer-review process of some sort (which may or may not be free for the author). Let's assume that manuscript is accepted for publication by the journal. The journal "publishes" the manuscript, at which point it is included in print and online versions. The manuscript can be accessed through a direct subscription to the journal or to a publishing house like Elsevier. These subscriptions are very expensive.

So the scientist pays to provide content and the reader pays to view it. What exactly does the publisher do?

This isn't meant to be exhaustive (I wrote about it a bit more here), but one definitely feels a little icky thinking about where all that money goes.

In today's Guardian, Harvard University notes that it can no longer keep up with the costs of maintaining a comprehensive database of journals. In real terms, this means Harvard students/faculty/physicians don't have access to all new information. If Harvard, with its multi-billion dollar endowment, can't keep up with rising costs, there's no doubt this system is in trouble.

We at OSK are glad to see Harvard is thinking progressively. We're disappointed it's only doing so for financial reasons. Such is life, I suppose.

Friday, March 30, 2012

Data dump

At OSK, we love data.

Big ups to the Obama administration for a $200 million data dump.

Tuesday, February 28, 2012

Research Works Act defeated

Huge success toward preserving the open science movement's momentum.

The Research Works Act would've set the open science movement back years by restricting congress from requiring that research created at the tax payer's expense be made publicly available. More clearly: the Research Works Act would've prohibited congress from requiring tax payer-funded science be made available for free to the tax payer.

I couldn't find a good summary in our "paper of record," so please check out the article here.

Also worth noting is the (originally) unconditional support for this bill by Elsevier, a publishing conglomerate. I'm not sure their support of it can be construed as anything but self-preservation, greed, taking a cut of the pie, a desperate act by an unnecessary middle-man.

I ask again: why do we need publishing houses? Why do we even need journals?

We do not. We need an effective, rigorous peer-review process that'll provide transparent, high-quality scientific publishing. This absolutely does not need to be accomplished via publishing houses and journals. We have other options.

Thursday, February 23, 2012

Saturday, February 18, 2012

Boycott publishing?

A great little piece from our northern neighbor on the absurd financial entanglements of the publishing industry. The backlash against academic status quo is clearly growing.

We still need a better system with which to publish.

Sunday, February 12, 2012

The Cautionary Tale of Anil Potti

Anil Potti is a former Duke University researcher who was one of the catalysts for the promise of chemotherapy genomics, i.e. decoding a patient's cancer's genome and picking out which chemotherapy would work best at killing it. It's an amazingly fascinating concept and it's still actively pursued to see if there is something to salvage. The reason there is something needing to be salvaged, however, is because Dr. Potti fabricated data. All of it. This was going to be the 'next big thing' in medicine, right up there with regenerative medicine, as the panacea to one's (cancerous) ills. Thankfully other diligent researchers closely examined the data and found incongruities and finally brought the sham of research down. If there was a more open source method to data review, perhaps these inconsistencies would have surfaced sooner. Because of the current system's behind-closed-doors policy, real people were subjected to faulty research premises. While it has yet to be shown if the patients did not receive true standard-of-care, it begs the question. Open Science: it can save lives.

You can learn more about Dr. Anil Potti here, here, and here.

Also, you can look up Dr. Potti and find several websites full of stock photo images of doctors and smiling young people as he details all of his grand exploits and gleans over his recent misconduct. He also falsely claimed he was a Rhodes Scholar. So yeah, he's a real piece of work.

Thursday, February 9, 2012

Federal Research Public Access Act

Here is an interesting article about the Federal Research Public Access Act. It provides links to a .pdf file that's 7 pages of the actual bill, which opens up federally-funded research to public access six months after publication (i.e. a really thoughtful name to the bill). What is great about this is that it follows on the heels of the Research Works Act, which would have effectively destroyed such a possibility and nullified the NIH open access policy. The latter bill was backed by Elsevier Publishing and stinks to high heaven; already numerous scientists have signed a boycott of Elsevier Publishing. Read on and contact your state representatives to support FRPAA and squash RWA.

Wednesday, January 18, 2012

Shelve SOPA

We at OSK strongly support the free exchange of information and creativity. We are amateurs at blogging and consequently can't figure out how to black out our site in protest of SOPA/PIPA, but below is a link telling you what you can do to help the movement to do so.

Tuesday, January 17, 2012

Open science in the public eye

I have many, many thoughts on open publishing. For now, here's the article:

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