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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.


In the end, basically he compared his daughter’s exome to that of everyone else in the family. By comparing in such a fashion he managed to zero in on a possible causal mutation. This is awesome (the fact that now they know, not the mutation itself). In the near future (~2 years) I plan to have everyone in my daughter’s pedigree sequenced to a high degree of accuracy so that I can trace with precision the sequence of de novo mutations which make each individual distinctive. Not only that, but it may be useful in the future in assessing possible disease risks unique to a given individual.

Hugh Reinhoff told his story at the Open Science Summit. I don’t think open and DIY science is going to be the whole future, but it is going to be a substantial part of the future. There are just some things that you as an individual have strong incentives to do which you can’t get others interested in. Additionally, collaborative open source science is probably one major push on the margins to make those selling services be more professional and add genuine value. If any reader in the Valley is excited about this sort of project you might want to contact Joseph Jackson. He’s got a lot of ideas and enthusiasm, and is genuinely interested in making a difference in peoples’ lives with a new “bottom-up” paradigm. I’m normally skeptical of such populism, but I’m not entirely happy with the status quo, so a shake up might do science some good.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Open science, Personal Genomics 
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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:

You can try and cut & paste this, but you’d come off as a fool if you didn’t know what you were talking about. The Coop lab has put up a substantial number of their quant bio papers up on arXiv, and I’m skeptical that that’s resulted in other groups cheating off them. On the contrary, in an idealized scientific environment the spread of insight will have spillover effects, positive externalities. The scientific community is one where there should be greater returns to scale due to the synergistic power of cross-fertilization.

On the other hand there is the flip side of this: the recent rash of data fraud and fudging impacting some of the more ‘empirical’ sciences. The community of science is based on trust, and sometimes I wonder how it persists. When the juice is in the collection and publication of data, rather than clever or deep analysis of data already commonly circulated, one can see the margin on cheating the system, or hoarding your cache.

I don’t have any clever solutions for how to prevent cheating in medical or psychological science. But I can hope that in the future genomic data sets will be constantly liberated, so that everyone is working from the same general script. And faking genomic data so that it would pass muster probably isn’t worth the time and energy. If you can manage to do this I think there’s a much better angle in going to Wall Street and screwing others for profit rather than scientific small-time fame.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Open science 
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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.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Open science, Personal Genomics 
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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.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: ArXiv, Open science 
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Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"