We need a GitHub of Science • Hacker News Board

Re: We need a GitHub of Science

#31

Post by wgrover » Sat, Apr 09, 2011, 3:14 AM UTC

mechanical_fish wrote: post #23

I'm a former biophysics postdoc myself. Now I work for an open-source software company. This post strikes me as charmingly naive. You have to love this guy. And yet any essay that discusses the incentive structure of science but doesn't use the word "grant" until the last sentence is beating around the bush. Follow the money, my friends. The publications are a side issue. To the extent that your count of top-tier pub…

Your "desk drawer in Tech Square" analogy is apt -- right now our publications are locked in a handful of those drawers, and folks can't even open the drawers unless they've bought keys from Springer/Elsevier/ACS/AIP/ACM/IEEE/etc. And how do we find out what's in the drawers? Searching the databases owned by ISI/Thompson-Reuters and friends, again for a fee.

Sure, a "Github of science" wouldn't turn anyone's basement into a cancer research lab, but it would mean that a lot of researchers at less-affluent universities would finally have full access to the literature of science.

Re: We need a GitHub of Science

#32

Post by chancho » Sat, Apr 09, 2011, 3:14 AM UTC

guygurari wrote: post #24

I'm a Ph.D. student working in theoretical high-energy physics. In this field we don't rely on peer-reviewed journals. Instead, when a researchers wants to "publish" a paper she uploads it to the arXiv, and the paper appears on the site within a day or two. The arXiv is open in the sense that almost anyone can publish there [1]. Researchers in the field catch up on new research by scanning the arXiv daily for interes…

"In this field we don't rely on peer-reviewed journals...papers are also published in journals, but I believe this is a formality that has more to do with obtaining grants and such than with actual communication within the community."

So peer reviewed journals are only important for grants, but your community doesn't rely on peer reviewed journals. Do you not rely on grants? Who funds your work? Do you all work for free, in your spare time?

Re: We need a GitHub of Science

#33

Post by marciovm123 » Sat, Apr 09, 2011, 3:18 AM UTC

guygurari wrote: post #24

I'm a Ph.D. student working in theoretical high-energy physics. In this field we don't rely on peer-reviewed journals. Instead, when a researchers wants to "publish" a paper she uploads it to the arXiv, and the paper appears on the site within a day or two. The arXiv is open in the sense that almost anyone can publish there [1]. Researchers in the field catch up on new research by scanning the arXiv daily for interes…

Thanks for the perspective. My impression from reading about Grigori Perelman was that almost all papers in arXiv are eventually published in traditional journals, for grant purposes, as alluded to by mechanical_fish. Maybe arXiv just needs to hire Scott Chacon (VP of R&D at GitHub).

Re: We need a GitHub of Science

#34

Post by chancho » Sat, Apr 09, 2011, 3:28 AM UTC

wgrover wrote: post #31

mechanical_fish wrote: post #23

I'm a former biophysics postdoc myself. Now I work for an open-source software company. This post strikes me as charmingly naive. You have to love this guy. And yet any essay that discusses the incentive structure of science but doesn't use the word "grant" until the last sentence is beating around the bush. Follow the money, my friends. The publications are a side issue. To the extent that your count of top-tier pub…

Your "desk drawer in Tech Square" analogy is apt -- right now our publications are locked in a handful of those drawers, and folks can't even open the drawers unless they've bought keys from Springer/Elsevier/ACS/AIP/ACM/IEEE/etc. And how do we find out what's in the drawers? Searching the databases owned by ISI/Thompson-Reuters and friends, again for a fee. Sure, a "Github of science" wouldn't turn anyone's basement…

Where do Google Scholar and CiteSeer fit into this analogy?

Can't speak for other fields, but in CS any outlet worth submitting to will let you post a preprint on your own website, and from there Google Scholar will pick it up and place the link to your free copy right next to the paywall link. It's not a perfect system---it's like an extreme form price discrimination, like when Microsoft turns a blind eye to piracy in emerging markets---but it does give access to those who can't pay, and its not as dystopian as you make it out to be.

Re: We need a GitHub of Science

#35

Post by guygurari » Sat, Apr 09, 2011, 3:38 AM UTC

chancho wrote: post #32

guygurari wrote: post #24

I'm a Ph.D. student working in theoretical high-energy physics. In this field we don't rely on peer-reviewed journals. Instead, when a researchers wants to "publish" a paper she uploads it to the arXiv, and the paper appears on the site within a day or two. The arXiv is open in the sense that almost anyone can publish there [1]. Researchers in the field catch up on new research by scanning the arXiv daily for interes…

"In this field we don't rely on peer-reviewed journals...papers are also published in journals, but I believe this is a formality that has more to do with obtaining grants and such than with actual communication within the community." So peer reviewed journals are only important for grants, but your community doesn't rely on peer reviewed journals. Do you not rely on grants? Who funds your work? Do you all work for f…

I guess I wasn't clear enough. What I mean is that the communication within the community, and the reputation of a researcher among her peers, does not rely on publications in reviewed journals. These are the things that can be compared with open-source development.

If researchers also need to publish their work in journals, write grant proposals etc., how is it relevant to the idea of applying the GitHub model to science? Of course raising money is part of the job for a professor, but thanks to the arXiv it's decoupled from the actual research work. It's at a point where I, as a Ph.D. student, have no reason to consider publishing in reviewed journals. This is in contrast to my friends in optics or condensed matter, for whom a publication in Nature or Science practically guarantees a good postdoc position.

Re: We need a GitHub of Science

#36

Post by sunir » Sat, Apr 09, 2011, 3:39 AM UTC

My goal for http://bibdex.com is to be this. I based the software on a wiki (original name was Bibwiki). The idea was to build lit reviews on topics that you could reuse and share with colleagues privately or publicly with the world.

I realized after starting that scientific communication is more complex, or at least it tries to be for various reasons. I could use help learning what people want from such a system.

I am keen on feedback or insights to drive my development. Please, if you are interested, you can reach me at sunir at bibdex com.

Re: We need a GitHub of Science

#37

Post by impendia » Sat, Apr 09, 2011, 3:39 AM UTC

guygurari wrote: post #24

I'm a Ph.D. student working in theoretical high-energy physics. In this field we don't rely on peer-reviewed journals. Instead, when a researchers wants to "publish" a paper she uploads it to the arXiv, and the paper appears on the site within a day or two. The arXiv is open in the sense that almost anyone can publish there [1]. Researchers in the field catch up on new research by scanning the arXiv daily for interes…

As a mathematics postdoc -- there is one (and only one) reason to publish your work in peer-reviewed journals. To prove to people outside your immediate area that you've done good work.

They are completely superfluous for disseminating knowledge.

Re: We need a GitHub of Science

#38

Post by dougabug » Sat, Apr 09, 2011, 3:52 AM UTC

mbreese wrote: post #27

dougabug wrote: post #25

Earlier quoted context omitted.

Do you need exclusive access to your very own scanning multiphoton microscope? Seems like laboratory virtualization would go hand in hand with open source science.

You may not need exclusive access to one, which is why a lot of institutions setup "centers" for this type of work (center for visualization, for example). Then multiple people can share the equipment and cost - if you can recruit people with a similar research focus. So, you may not need one exclusively, but you do need one locally available.

Seems like many samples could be prepared locally and shipped to the analysis center ala Netflix. Another possibility would be making samples to order at a location near where the necessary equipment is located. For instance, I need a brain tissue sample from xxx type of mouse, infected with pathogen yyyy.

Re: We need a GitHub of Science

#39

Post by dougabug » Sat, Apr 09, 2011, 3:58 AM UTC

mechanical_fish wrote: post #30

dougabug wrote: post #25

Earlier quoted context omitted.

Do you need exclusive access to your very own scanning multiphoton microscope? Seems like laboratory virtualization would go hand in hand with open source science.

You can share them. Many labs do. Indeed, most of these things are probably shared in one way or another. And you're correct: The trick to encouraging open source science is not to focus on the social networking tech -- that will be ready when you need it -- but to first attack the problem of doing quality lab work on the cheap. That's where the bottleneck is. The biggest problem with shared facilities is the tragedy…

The cost of maintaining your own tools is quite high, as is the expertise required to maintain them in working order. It seems to be that the inexperience or lack of skill which leads to shared equipment getting ruined is due to the fact that extremely sensitive equipment is being handled by students and junior scientists with little engineering background. The same argument could be made for the value of having your own servers. The scientific equivalent of a datacenter, would necessarily entail staffing of highly qualified, experience personnel. Such expertise would undoubtedly be costly, but it would be amortized over a large amount of equipment.

Re: We need a GitHub of Science

#40

Post by wgrover » Sat, Apr 09, 2011, 4:01 AM UTC

chancho wrote: post #34

wgrover wrote: post #31

Earlier quoted context omitted.

Your "desk drawer in Tech Square" analogy is apt -- right now our publications are locked in a handful of those drawers, and folks can't even open the drawers unless they've bought keys from Springer/Elsevier/ACS/AIP/ACM/IEEE/etc. And how do we find out what's in the drawers? Searching the databases owned by ISI/Thompson-Reuters and friends, again for a fee. Sure, a "Github of science" wouldn't turn anyone's basement…

Where do Google Scholar and CiteSeer fit into this analogy? Can't speak for other fields, but in CS any outlet worth submitting to will let you post a preprint on your own website, and from there Google Scholar will pick it up and place the link to your free copy right next to the paywall link. It's not a perfect system---it's like an extreme form price discrimination, like when Microsoft turns a blind eye to piracy…

I think that CS is a lot more open than other fields, even putting preprints online and soliciting feedback before publication (that's unheard of in chemistry and biology). You're right that some authors put PDFs of their papers on their websites and Google Scholar finds them, but I frequently need papers that I can only get through interlibrary loan (and I work at MIT; even a relatively wealthy university can't afford everything).