Baylor releases Exome and WGS data of 7 cancer patients with Open Access

An open access pilot freely sharing cancer genomic data from participants in Texas

• Scientific Data 3, Article number: 160010 (2016) 
• ​doi:10.1038/sdata.2016.10
•  In a pilot Open Access (OA) project from the CPRIT-funded Texas Cancer Research Biobank, many Texas cancer patients were willing to openly share genomic data from tumor and normal matched pair specimens. For the first time, genetic data from 7 human cancer cases with matched normal are freely available without requirement for data use agreements nor any major restriction except that end users cannot attempt to re-identify the participants (http://txcrb.org/open.html).

There's whole exome seq data and 2 whole genome sequencing data where the sample quality is good enough for WGS.

A copy of the open-access TCRB data, conditions of use, and the HGSC’s Mercury informatics pipeline is available now for DNAnexus Platform users.

The full paper is here http://www.nature.com/articles/sdata201610

A copy of the data is also available for DNAnexus Platform users here https://dnanexus.github.io/tcrb-data/

Nature Special:"The Future of Publishing"

The fact that NPG has published a special on "The Future of Publishing" shows that change is underway. The special gives a balanced view including M. Eisen's views (as reported by Van Noorden The True Cost of Science Publishing ) but naturally the message that they wish to convey is in the last (concluding) article in the series.

“As a young investigator you have to do what's economically viable,” says Stephen Macknik, a neuroscientist at the Barrow Neurological Institute in Phoenix, Arizona. Paying an article-processing charge for a reputable open-access journal may be a good middle ground for young researchers, he says.
But scientists shouldn't sacrifice funding that was meant for research. “To maximize their competitiveness it is vital that young researchers maintain a productive profile of high-quality research, and this means using research funds to do as much high-quality research as possible,” says Chambers. “It falls to the more senior scientists to change the system.”

EDITORIAL

• Disciplinary action

  How scientists share and reuse information is driven by technology but shaped by discipline.

  Nature ( 28 March 2013 )

NEWS

• Sham journals scam authors

  Con artists are stealing the identities of real journals to cheat scientists out of publishing fees.

  Nature ( 28 March 2013 )

NEWS FEATURES

• The true cost of science publishing

  Cheap open-access journals raise questions about the value publishers add for their money.

  Nature ( 28 March 2013 )

• The library reboot

  As scientific publishing moves to embrace open data, libraries and researchers are trying to keep up.

  Nature ( 28 March 2013 )

• The dark side of publishing

  The explosion in open-access publishing has fuelled the rise of questionable operators.

  Nature ( 28 March 2013 )

COMMENT

• Beyond the paper

  The journal and article are being superseded by algorithms that filter, rate and disseminate scholarship as it happens, argues Jason Priem.

  Nature ( 28 March 2013 )

• A fool's errand

  Objections to the Creative Commons attribution licence are straw men raised by parties who want open access to be as closed as possible, warns John Wilbanks.

  Nature ( 28 March 2013 )

• How to hasten open access

  Three advocates for a universally free scholarly literature give their prescriptions for the movement’s next push, from findability to translations.

  Nature ( 28 March 2013 )

BOOKS AND ARTS

• Q&A: Knowledge liberator

  Robert Darnton heads the world's largest collection of academic publications, the Harvard University Library system. He is also a driver behind the new Digital Public Library of America. Ahead of its launch in April, he talks about Google, science journals and the open-access debate.

  Nature ( 28 March 2013 )

CAREERS

• Open to possibilities

  Opting for open access means considering costs, journal prestige and career implications.

  Nature ( 28 March 2013 )

Are we slaves to the scientific publishing industry?

Found this fascinating analogy in the post http://conservationbytes.com/2012/01/29/knowledge-slavery/

...our slavery to the scientific publishing industry.

And 'slavery' is definitely the most appropriate term here, for how else would you describe a business where the product is produced by others for free¹ (scientific results), is assessed for quality by others for free (reviewing), is commissioned, overviewed and selected by yet others for free (editing), and then sold back to the very same scientists and the rest of the world's consumers at exorbitant prices.

This isn't just a whinge about a specialised and economically irrelevant sector of the economy, we're talking about an industry worth hundreds of billions of dollars annually. In fact, Elsevier (agreed by many to be the leader in the greed-pack – see how some scientists are staging their protest; also here) made US$1.1 billion in 2010!

what are your thoughts? I don't think that making money is necessarily bad, but apparently rich is even a derogatory term now, with rich ppl (oops) preferring to be called high net worth individuals. But when it's larger entities, corporations, it might be easy to mud sling them.
However, I think the author has a point when making the analogy, my 1st shock was discovering that I have to read lengthy copyright info on what I can or cannot do with something that I researched / wrote  (see http://www.elsevier.com/wps/find/authorsview.authors/rights )

It's so much easier to understand from a photographer's point of view
http://www.photosecrets.com/photography-law-copyright

"Copyright" is "the right to copy." This right is a legal construct, designed for you — the artist — to support your artistic endeavors. Without copyright, people would be free to use your artistic work
You can negotiate a "license" to copy, and perhaps even get paid in real money. Hopefully this will give you more incentive to create art, and the world will be a better place.

Will People Steal My Work?

Generally no, as publishers live by copyright law and usually have established rates which they gladly pay. A more likely problem is that publishers may not know that you are the copyright owner, which goes back to that "©" symbol and digital watermark.

Hey wait a minute .. "the world will be a better place "  hmmm I thought scientists are the ones trying to help the world with advancing human knowledge where our incentive to churn out more scientific results?

hmmm food for thought ..
Post comments!

Scientists, Share Secrets or Lose Funding: Stodden and Arbesman - Bloomberg

This article expresses my views in a much more eloquent way

The Journal of Irreproducible Results, a science-humor magazine, is, sadly, no longer the only publication that can lay claim to its title. More and more published scientific studies are difficult or impossible to repeat.
It’s not that the experiments themselves are so flawed they can’t be redone to the same effect -- though this happens more than scientists would like. It’s that the data upon which the work is based, as well as the methods employed, are too often not published, leaving the science hidden.

Too Little Transparency

Consider, for example, a recent notorious incident in biomedical science. In 2006, researchers at Duke University seemed to have discovered relationships between lung cancer patients’ personal genetic signatures and their responsiveness to certain drugs. The scientists published their results in respected journals (the New England Journal of Medicine and Nature Medicine), but only part of the genetic signature data used in the studies was publicly available, and the computer codes used to generate the findings were never revealed. This is unfortunately typical for scientific publications.
The Duke research was considered such a breakthrough that other scientists quickly became interested in replicating it, but because so much information was unavailable, it took three years for them to uncover and publicize a number of very serious errors in the published reports. Eventually, those reports were retracted, and clinical trials based on the flawed results were canceled.
In response to this incident, the Institute of Medicine convened a committee to review what data should appropriately be revealed from genomics research that leads to clinical trials. This committee is due to release its report early this year.
Unfortunately, the research community rarely addresses the problem of reproducibility so directly. Inadequate sharing is common to all scientific domains that use computers in their research today (most of science), and it hampers transparency.
By making the underlying data and computer code conveniently available, scientists could open a new era of innovation and growth. In October, the White House released a memorandum titled “Accelerating Technology Transfer and Commercialization of Federal Research in Support of High-Growth Businesses,” which outlines ways for federal funding agencies to improve the rate of technology transfer from government-financed laboratories to the private business sector.


As Jon Claerbout, a professor emeritus of geophysics at Stanford University, has noted, scientific publication isn’t scholarship itself, but only the advertising of scholarship. The actual work -- the steps needed to reproduce the scientific finding -- must be shared.  


read the full article at http://www.bloomberg.com/news/2012-01-10/scientists-share-secrets-or-lose-funding-stodden-and-arbesman.html

Posting of Ion Torrent protocols online is a violation of Terms and Conditions

http://seqanswers.com/forums/showthread.php?t=10400

Just got to know of this rather disturbing fact that seqanswers admins were informed (nicely) to take down online posted protocols for the Ion Torrent.

I wished to post the adaptor sequences for RNA multiplex libraries online before as a help for bioinformaticians that might have gotten their data from a service provider or have problems getting a prompt response from the ever friendly FAS. I mean if it's online, I need not bother them yeah?

Now I wonder if I might be violating terms and conditions somewhere out there.


I would argue for posting of protocols online.
Lab Protocols are meant to be optimised in every lab.
case in point? you promote active discussion on the product and once you have that, it is an active support community that beats a whole army of FAS with trained responses to problems in protocols.
see this imaginary conversation

Researcher A: making that incubation step longer for 10 secs improves your yield? good for you! but it didn't work for me, any advice on where else I can do it?
Researcher B: yeah sure, you see page 15 step 8A ? don't over do that step as it affects yield but be warned it might affect the quality of the final output but let's solve one problem at a time. . I tried that last week!

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

Visualization of orthogonal (disjoint) or overlapping datasets is a common task in bioinformatics. Few tools exist to automate the generation of extensively-customizable, high-resolution Venn and Euler diagrams in the R statistical environment. To fill this gap we introduce VennDiagram, an R package that enables the automated generation of highly-customizable, high-resolution Venn diagrams with up to four sets and Euler diagrams with up to three sets.

A Boycott for NPG journals?

NPG as in Nature Publishing Group for those not in the know, this includes the journal Nature. What might have sparked off this?
An impending price increase of 400% for journal subscription.

Michael Eisen, nailed it down it his blog post.
I totally agree with his view especially how he describes the situation as:
"Only one thing — short of outright insanity — can lead a company to think they can get away with this kind of behavior: a monopoly. And it is the monopolistic, and grossly unfair and irrational, business model that NPG and most other scientific publishers employ that should be the real target of any organized action from UC faculty."

Jonathan Eisen also has interesting things posted here

I think the price increase might be a good move to persuade researchers to use soft copies of journals instead of having to resorting to print. But as Michael rightly points out. It shouldn't be an issue of price. And price increase in this climate, I think NPG might be making a wrong move here.

What are your thoughts? Would you adhere to such a boycott if your department is against the idea?