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We need a GitHub of Science

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Re: We need a GitHub of Science

#41

Post by mechanical_fish »

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…

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. Far older things, like TeX, were invented for this purpose. Nowadays we have everything from PLoS to arXiv to Google Scholar to custom in-house blogs to PDFs sent through email.

The continued existence of for-profit journals is an economic, political, and anthropological problem, not a technological one. PLoS and the like are slowly changing things, but I still suspect that the only way to free our journals within less than a generation or two is to lobby (e.g.) the NIH to require that their funded projects be published in free journals. When a grant agency talks, people listen. When postdocs talk, alas, it makes a very subtle sound. ;)

Re: We need a GitHub of Science

#42

Post by ippisl »

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…

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 reduced prices.

2. students took pictures of earth from space using £90 in equipment.

3. a diy electron microscope, a guy made himself [1], probably costs a lot less then commercial ones.

There many more extremely cheap stuff like this. Maybe the first place of open sourcing science is in support of open source tool development.

[1] http://blog.makezine.com/archive/2011/03/diy-scanning-electr...

Re: We need a GitHub of Science

#43

Post by ylem »

dougabug wrote: post #39
mechanical_fish wrote: post #30

Earlier quoted context omitted.

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…

Staffed by who? There are actually some user facilities for materials synthesis--the problem is that if someone is making someone else's material instead of working on something that they're interested in, then I don't think that you're going to get the same level of productivity out. Also, materials synthesis takes time and running through lots of dead ends. When I was a grad. student, a postdoc from a collaboration would drive in to our lab with powders she had made--try to grow a crystal for a week (sleeping for maybe an hour or two a night on a floor in our office) and then go back to her home institution and come back in a few weeks. That just doesn't work--you don't have the responsiveness to be able to figure out what dead ends you're wandering down...Imagine if you were writing code and could only run it once every few weeks. Now, imagine that it was thousands of lines of nontrivial code and you're trying to debug it that way...

Re: We need a GitHub of Science

#44

Post by archgoon »

dougabug wrote: post #25
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…

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.

My lab has a SEM. It costs $50/hour to operate. I have been led to understand that most of that cost is to cover if something goes wrong (which means we can't lower the per hour cost by having more people use it).

Think how much more expensive coding would be if it cost $50/ per compile (or hell $10/per compile).

Re: We need a GitHub of Science

#45

Post by stewbrew »

thisrod wrote: post #21

The programs on Github were written by amateurs. Professionals can do better - compare Python, PHP and Gnuplot to Mozilla, Scheme, Haskell, Plan 9 and Mathematica. But evidently people can keep their day jobs and still write good programs. Science is different. The amateurs are called cranks, and a small community of professionals does the good stuff. (There are exceptions, but few.) The basic issue is who will pay t…

You're mixing language definitions and implementations. You're comparing software that was created by big companies with software created by small teams or single developers. I think good commenters can do better.

BTW you're implying governments are funding over-priced journals people outside of prestigious institutions cannot afford. Even though that's true it's not the way it should be.

Re: We need a GitHub of Science

#46

Post by dougabug »

ylem wrote: post #43
dougabug wrote: post #39

Earlier quoted context omitted.

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…

Staffed by who? There are actually some user facilities for materials synthesis--the problem is that if someone is making someone else's material instead of working on something that they're interested in, then I don't think that you're going to get the same level of productivity out. Also, materials synthesis takes time and running through lots of dead ends. When I was a grad. student, a postdoc from a collaboration…

Staffed by scientists and engineers, I imagine. You can get some pretty sophisticated parts built by foundries. At one point, making a microchip was prohibitively expensive. Nowadays, when you create chips basically by coding them in high level synthesis languages. Spinning a chip does take weeks. Obviously when a process takes longer to carry out, with high iteration cost, careful methodology is called for. Simulation and error checking software becomes valuable. Heck, once upon a time computers themselves were massively expensive, among the most expensive machines built. Computing wasn't born cheap. Mass production and decades of technological advances made them so. Machines for combinatorial science may someday be more effective than graduate students.

Re: We need a GitHub of Science

#47

Post by SoftwareMaven »

thisrod wrote: post #21

The programs on Github were written by amateurs. Professionals can do better - compare Python, PHP and Gnuplot to Mozilla, Scheme, Haskell, Plan 9 and Mathematica. But evidently people can keep their day jobs and still write good programs. Science is different. The amateurs are called cranks, and a small community of professionals does the good stuff. (There are exceptions, but few.) The basic issue is who will pay t…

Most of the interesting projects on Github were written by professionals and are far better quality than the average "professional" day-job application because it is a developer's passion and not constrained by business development.

I do not believe open source solves all problems, but you dismiss the incredible value and quality of so much that I find it difficult to take the rest of the comment seriously.

It sounds more like "People with credentials (whether scientists or professional programmers) are the only people who can produce quality work. I have credentials. I'm part of the elite who can do quality work."

Re: We need a GitHub of Science

#48

Post by dougabug »

archgoon wrote: post #44
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.

My lab has a SEM. It costs $50/hour to operate. I have been led to understand that most of that cost is to cover if something goes wrong (which means we can't lower the per hour cost by having more people use it). Think how much more expensive coding would be if it cost $50/ per compile (or hell $10/per compile).

$50/hr seems quite reasonable. I doubt I'd need more than 100 hours a year of use, and even if I required several hundred hours, that's still readily affordable.

Re: We need a GitHub of Science

#50

Post by ramanujan »

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…

I used to think this as well. But if you think about things which are ridiculously expensive -- like cars or airplanes or Google's datacenters -- all of them got their start in someone's garage.

After spending some time with the Open Wetware/DIYBio guys, I realized that no one (other than the DIYBio guys) has really spent time reducing the costs of the fundamental toolkit of the molecular biologist.

Now they are starting to do so:

http://openwetware.org/wiki/DIYbio:Notebook/Open_Gel_Box_2.0...

That gel box is going to be about $200-$300 all in. You might not get a multiphoton microscope right off the bat, anymore than you'd get access to all of Goog's servers when you were just starting out with your laptop...but reducing the price of entry for the hobbyist biologist/biochemist to say $5k or less is going to be really important.

That's because the role of the DIYBio community is set to wax in a big way. With the NIH budget cuts and the coming fiscal collapse of the US Government, the sun is about to set on a ~70 year period (1945-2015) of centralized US government research. The period before 1945 was more innovative by many measures (e.g. http://www.nytimes.com/2011/01/30/business/30view.html?_r=1), and potentially the period afterwards will be as well.

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