

People not liking open source (and it's not Oracle) - Garbage
http://weblogs.java.net/blog/fabriziogiudici/archive/2010/11/07/people-not-liking-open-source-and-its-not-oracle

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dododo
in my experience, it's common in academia for code to "float around". often
it's not officially open source or distributed, but you know someone who has
the code for some paper, so you can use it. there's even a few textbooks in
this state (for years).

i think the real reason for not releasing this code is time---you might be
surprised at just how much effort goes into making a paper/talk/article
polished. sure, you could just release the hacky code you used to do your
calculations, but you'd like so much more---for it to be useful, for it to be
a credit to you, for it to also do XYZ. research code is efficient in that it
gets exactly what you want for the paper; it's rarely usable by anyone else.
there is essentially zero payoff in academia in publishing code, and so
there's no time to fulfill these desires.

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araneae
Exactly. In my experience, if someone wants to look at your code, they will
e-mail you and ask for it. Then you e-mail it to them.

Sharing on something like sourceforge just simple isn't done. It's not because
scientists are "cheating," it's because it's not part of the culture.

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scott_s
Another conclusion is that scientists gain very little by publishing their
code. In research terms, they're evaluated on published papers, receiving
grants and graduating students. The incentives just aren't there.

~~~
ntoshev
Are there incentives to have a lower/higher barrier for someone else to
reproduce your findings and build on them?

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dkarl
If you have no reputation and results that contradict expectations, you
definitely want someone to reproduce your work. Otherwise, people may follow a
Bayesian argument and decide the mostly likely conclusion is that your work
sucks.

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tensor
I think it's worth pointing out that taking someones code and running it again
on the same data does not constitute an independent verification of the
original work. Just like scientists don't go using the same lab to verify an
experiment, they shouldn't use the same code.

That said, it is often useful to release code for other reasons. For applied
areas, releasing the code in the form of a software tool is fairly common.
This allows people from the target area, who may not be computer scientists,
easy access to the new method.

Code review seems to be nearly non-existent in the scientific community,
although it does happen occasionally when one researcher uses another's code
base for further experimentation.

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JoelMcCracken
Investigating the world through computation is a relatively new phenomenon for
science.

Science is discussed and advanced through papers. These papers aren't an exact
recording or rendition of what was accomplished, but a discussion of the idea,
methods used, and eventually a conclusion. Methods may be algorithms, but it
doesn't necessarily mean the actual source code.

The idea is that the actual code that a scientist used isn't terribly
valuable. If another scientist wants to verify the conclusions, they should
just whip up another bit of code (or, do the same experiment) themselves.

Asking for scientists to contribute source code is not wrong, it just isn't
done (to my knowledge) with other modes of scientific exploration.

~~~
possibilistic
This isn't something new at all! Chemists have been using computers
extensively since the 70's, and this can be evidenced by the fact that several
physical chemists at my university still use Fortran. Computers have been used
in science from their inception. Only now are they becoming indespensible for
molecular biologists--but they still have a long way to go in both terms of
parallelism and the related tools to be really practical for the intense
intermolecular interactions we deal with.

Why don't we publish our code? Do you publish one-off shell scripts or
database migration code? The only important code is already open source or is
(unfortunately) commercial in nature.

~~~
josegonzalez
I regularly see dotfiles in github repositories.

Maybe there is a barrier to adoption in the form of git. A more polished
version of Gist - marketed to scientists and researchers - would increase
uptake.

~~~
eru
What do you mean by "see[ing] dotfiles"?

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bbb
> I can only conclude that many scientists are not confident at all with their
> theories, or they are purportedly cheating.

That's really not an insightful conclusion. I think it's rather a question of
pride and effort: the code probably needs to be cleaned up before release, and
the reward for investing that time is very low (career-wise). Researchers are
going to publish their source code when it becomes required by most major
journals and conferences.

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bhickey
I've worked as an academic hacker.

Amongst dedicated biologists, there's no motivation to release your source
code. It's the job of a biologist to publish papers so that he or she can pull
down the next grant. Anything that doesn't further this goal is going to get
zero traction.

Publishing it doesn't help you get into Nature or Science. Sure, Sean Eddy
(www.psc.edu/general/software/packages/hmmer/) is going to release his code,
but he's a methods guy. The software is the focus of publication. The only way
code is going to get published is if the journals refuse to publish results
without code.

