Tag: Open science

One girl, one exome

By Razib Khan | October 22, 2012 12:22 am

Interesting story in The San Jose Mercury News, Open-source science helps San Carlos father’s genetic quest:

“We used materials that are public, freely available,” said Rienhoff, a physician and scientist, as Beatrice frolicked nearby. “And everything we’ve learned we’ve put back out there, in the public domain. It’s for the patient’s good, and the public good.”

Born with small, weak muscles, long feet and curled fingers, Beatrice confounded all the experts.

No one else in her family had such a syndrome. In fact, apparently no one else in the world did either.

Rienhoff — a biotech consultant trained in math, medicine and genetics at Harvard, Johns Hopkins and the Fred Hutchinson Cancer Research Center in Seattle — launched a search.

He combed the publicly available medical literature, researching diseases, while jotting down each new clue or theory. Because her ailment is so rare, he knew no big labs or advocacy groups would be interested.

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CATEGORIZED UNDER: Personal Genomics

You can't scoop someone else's brain

By Razib Khan | July 21, 2012 11:07 pm

arXiving our papers:

I, and I’m sure other people, have worried about being scooped and beaten to publication due our arXived papers. But really this is silly as we’ve usually given talks, posters, etc on them at big conferences, so the idea that people somehow don’t know about our work before it appears in print is ridiculous. It is far better to get work out, once you consider it worthy of publication, so it can be read and cited by others.

This is in reference to the paper The Geography of Recent Genetic Ancestry across Europe. Go and read the materials and methods. I’m sure that a substantial minority of the readers of this weblog have used every single piece of software listed therein. Phasing and such requires a little bit of computational muscle, but that’s not an impossible hurdle. Additionally, many readers with academic affiliations could get their hands on the POPRES data set. But the generation of a paper, from methods to results to discussion, is not simply a robotic sequence of running data through software or algorithms. You need a first-rate statistical geneticist (e.g., the authors) to actually assemble the pieces together together coherently and with insight even granting the fundamental units of the whole.

Then there are sections of the methods with explication such as this:

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An attempt at "open science"

By Razib Khan | August 31, 2011 3:09 pm

I was asked by the person who provided me the Tutsi genotype for detailed results. Of course I would do so! So I uploaded the raw csv files to Google Docs. The format and explanation isn’t totally clear, though if you follow my posts you’ll get it. This is for people who want more than pretty visualizations. But it did make me consider: I do many ADMIXTURE and EIGENSOFT runs, and you only see a small minority. This isn’t optimal for readers who want to dig deeper, but it also results in possible unconscious bias. So I’m going to try and do something different: I will post the raw results (at least in csv format) of all runs. But I obviously don’t want to cluster this weblog with updates, so you have to do one of two things to get notifications:

1) Follow me on twitter

2) Add me on Google+

At some point I might just start throwing stuff into a public folder, but that’s often so user unfriendly that only those “in the know” can decrypt what is what. My aim here is to resolve some confusions by posting all the results that I get to see. A lot of the discussion on online forums about my ADMIXTURE related postings are easy to answer if the people who are confused saw the full range of my results.

CATEGORIZED UNDER: Personal Genomics
MORE ABOUT: Open science

Where is the ArXiv for X?

By Razib Khan | August 30, 2011 1:36 pm

Derek Lowe asks “Why Isn’t There an ArXiv For Chemistry?” Where indeed. A few years ago I went to a talk given by Michael Eisen and asked him about why the biological sciences didn’t have an ArXiv, and one of his explanations was that intellectual property was more of a concern in this area (e.g., pharmaceutical funded research). That sounds plausible enough to me. But the existence of ArXiv still should serve as a starting point for people outside of the physical and mathematical sciences in terms of the possibilities. Much of the discussion around Joe Pickrell’s post ‘Why publish science in peer-reviewed journals?’ seemed to operate in a world where ArXiv didn’t exist. And it’s not just ArXiv, SSRN makes it easy to get papers in social science. We have the technology, and we see the possibilities. There are obstacles, but let’s not pretend as if we don’t have a model for some success.

MORE ABOUT: ArXiv, Open science

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

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