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We need a GitHub of Science

marciovm.com

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Re: We need a GitHub of Science

#61

Post by enjalot »

mechanical_fish wrote: post #41
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…

I loathe the for-profit journals as much as anyone, but I'm deeply suspicious of any hypothesis of the form "the reason why journals still cost money is that we haven't yet invented the right electronic social network for sharing scientific information". We've had the technology to publish science online for decades. We have tinkered with it dozens of times. The web was originally invented for exactly this purpose. F…

I agree with your statements, but perhaps the appeal of a github for science isn't the technology, it's the culture that comes with it. You can run your own git servers and submit patches over email, but when you can fork with the click of a button and do a pull request with another click, it encourages that much more sharing.

I've had this discussion with some of my professors, mostly just about open sourcing research code (I'm in Scientific Computing) and some of them wont do it because they want to squeeze a few publications out of one code and don't want anyone 'stealing' their publication. I find it disturbing, but it's ingrained in the culture. Changing it is important to me, but I don't see how yet.

Re: We need a GitHub of Science

#62

Post by ippisl »

mechanical_fish wrote: post #55
ippisl wrote: post #42

Earlier quoted context omitted.

I don't know much about expensive lab equipment, but if you follow the DIY world, or the open source world , or even indian/chinese innovators, you see people building physical stuff at fractions of the price of commercial stuff. A few example to illustrate my point: 1. Open farm tech - tractor and brick compressor and 1/3 to 1/10 of the commercial prices. they plan a whole set of manufacturing equipment at those red…

I now see a terrible flaw in my essay of last night: I took the cheap and easy rhetorical route of emphasizing the costs of the fanciest equipment. Whereas the thing that kills you in science budgeting is actually the mundane stuff that you need in vast quantities. Perhaps I should have talked about something boring, like absolutely clean, absolutely sterile containers. There is nothing sexy about containers and pipe…

Thanks for a very detailed and interesting description of the scientific process.

From the way you describe it, it seems that doing science in your area, is not the science that would attract small hacker groups , because it's long and boring.

hackers tend to contribute to the interesting parts of open source , i.e. languages like python and ruby, and organizations tend to do the big, boring heavy lifting, things like android , linux , etc.

By the way, what about technologies like combinatorial testing, automation , and miniturization ? what would be their affect on the way biology is done ?

Re: We need a GitHub of Science

#64

Post by Goladus »

ippisl wrote: post #62
mechanical_fish wrote: post #55

Earlier quoted context omitted.

I now see a terrible flaw in my essay of last night: I took the cheap and easy rhetorical route of emphasizing the costs of the fanciest equipment. Whereas the thing that kills you in science budgeting is actually the mundane stuff that you need in vast quantities. Perhaps I should have talked about something boring, like absolutely clean, absolutely sterile containers. There is nothing sexy about containers and pipe…

Thanks for a very detailed and interesting description of the scientific process. From the way you describe it, it seems that doing science in your area, is not the science that would attract small hacker groups , because it's long and boring. hackers tend to contribute to the interesting parts of open source , i.e. languages like python and ruby, and organizations tend to do the big, boring heavy lifting, things lik…

I wouldn't say it's boring. Not everyone has the patience science requires but for those that do, there's plenty of incentive to do disciplined data collection.

It's most likely just that the resources required to do it are still out of reach, unlike the python and ruby communities where your biggest expenses are a computer with a text editor and access to an internet connection.

Even some computing resources are out of reach for individuals, even if just barely. Amazon hosts public datasets, which is nice, but but the 500,000 instance-hours of HPC compute time needed to do analysis is not going to be in the budget of a hacker-in-the-basement (ie someone with no funding, whether it be from grants, revenue, or investment).

Re: We need a GitHub of Science

#65

Post by stevenbedrick »

mechanical_fish wrote: post #41
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…

I loathe the for-profit journals as much as anyone, but I'm deeply suspicious of any hypothesis of the form "the reason why journals still cost money is that we haven't yet invented the right electronic social network for sharing scientific information". We've had the technology to publish science online for decades. We have tinkered with it dozens of times. The web was originally invented for exactly this purpose. F…

The NIH is already actually doing that, at least sort of- any article reporting NIH-funded has to be submitted to PubMed Central, from where anybody can view and download the full text, figures, etc. I believe that there's an embargo exemption that allows journals to hold off on submitting to PMC for a few months or maybe up to a year, but after that it's public.

Right now, it's just NIH, but it's only a matter of time before AHRQ and the other biomedical funding agencies get in on the action, and there's no reason (in principle, anyway) why NSF or DOE couldn't also join in or do something similar on their own.

Re: We need a GitHub of Science

#66

Post by juretriglav »

Yes we do. Not just a replica of it with different content though, but a separate product tailored to the needs (and wishes) of science, sharing only some of the core ideas of GitHub. Sometimes I wonder if I should welcome the surfacing of ideas that have a large overlap with my own, or be anxious knowing that my lead has possibly been somewhat reduced.

Re: We need a GitHub of Science

#67

Post by serichsen »

The most pressing problem of our modern information society is the abundance of crap.

The service peer-review provides is the filtering of crap, so that not everyone has to do that by himself. This makes science possible, as not everyone can be a master of all trades.

Publication without review is called "journalism".

As a side note, I believe that Elsevier has acquired an extreme market dominance in the scientific publishing sector and is abusing it in alarming ways.

Re: We need a GitHub of Science

#68

Post by etree »

gsiener wrote: post #63

I just met the brains behind Opani ( http://opani.com ) last night and they are a huge step in this direction.

Opani is actually a huge step in the right direction. I think Marcio's post is fantastic. I would in fact add an additional idea to it.

In addition to the open prestige inherent in GitHub, there is also the fact that one's work is vetted by a community. It becomes very difficult if not impossible to publish crap and claim that it is quality. In science this is not the case. The peer review system is supposed to protect us against that. However, my understanding is that a surprising percentage of research in top ten journals can't be reproduced either because key details about implementation are missing or because it is actually not reproducible.

A GitHub for science could also meaningfully move the ball forward in making science reproducible as it should be easy to wrap ones scripts in a specification of an "environment" that can be readily setup, deployed, and run. A lot of work would be required to develop corollaries for non-computational scientific domains, but it would be a hugely valuable effort as discussed in the general reproducible research community (http://reproducibleresearch.net/).

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