5 ms·

Biology researchers don't get to reuse the other guy's mice, why should they reuse their code? As long as the paper describes the algorithms used, anyone should

Biology researchers don't get to reuse the other guy's mice, why should they reuse their code? As long as the paper describes the algorithms used, anyone should be able to duplicate the work using their own preferred implementation. Also, a lot of the code may well be specific to the apparatus used, which may be unique to a lab, consisting of custom-built hardware.

ajuc 15y ago
Mouse can't be perfectly copied. Code can. If biologists could copy mice from other experiment to give them their own drugs and compare results, they would surely do this along with using their own mice. The more ways to compare experiments, the more sure we will be about results. I understand cleaning up code is a lot of work, so don't do it, just release it as it is. I know it will be ugly, will include obscenity, etc. If somebody need it, it will do the rest of work.
- jonhendry 15y ago
  "The more ways to compare experiments, the more sure we will be about results." No. The more exactly you duplicate the original experiment, the more likely you duplicate any confounding issues. If someone observes something through a telescope, it's best to verify it through a different telescope somewhere else, to exclude the possibility of an optical quirk of the first telescope.
  - ajuc 15y ago
    Some people will run the same code on the same data. They will get the same results, but so what. Some other people will run the same code on different data (maybe from simulation, or when checking their own theory). They will get some other results, or the same. Some people will recreate experiment from scratch, and get code B and data B. Some people will run code A on data B. Some people will run code B on data A. Now we can't do that. The code is already written, it's waste to hide it, it's not like publishing code prohibit other people from writing their own code. That's how you check for errors - by changing as little as possible and observing results.
JonnieCache 15y ago
>Biology researchers don't get to reuse the other guy's mice In a sense, they actually do. https://secure.wikimedia.org/wikipedia/en/wiki/C57BL/6 https://secure.wikimedia.org/wikipedia/en/wiki/C57BL/6 https://secure.wikimedia.org/wikipedia/en/wiki/BALB/c https://secure.wikimedia.org/wikipedia/en/wiki/BALB/c
- jonhendry 15y ago
  They use identically-specified mice. They don't use the same mice. The mice used by one lab could, theoretically, be off-spec mutants. Or the lab could have made mixed up which mice they used. Saying you used a particular strain of mouse is like saying you used a particular algorithm on your data. Asking to use the exact individual mice used by another lab might not reveal an error such as mixed-up strains.
  - JonnieCache 15y ago
    Sure. I wasn't posting those links to further this argument, I posted them simply because they are interesting. Besides, they're only inbred strains, not clones.
    - jonhendry 15y ago
      They can also be pretty damned expensive. Like $400+ for a mouse.
      - JonnieCache 15y ago
        Looks like I'm in the wrong business. How does that come about? Patent shenanigans?
        jonhendry 15y ago
        Probably. But really, if you're spending $50,000 on an experiment, you're probably more interested in getting mice that are really what it says on the label, than in saving a few bucks and possibly shooting your experiment and/or career in the nuts. Pretty much anything 'lab grade' is going to be expensive. The lab I worked in ordered a lab grade laser for optogenetics experiments, and that cost something like $18k. Presumably that gets you a very precise, stable wavelength.

ajuc 15y ago

Mouse can't be perfectly copied. Code can. If biologists could copy mice from other experiment to give them their own drugs and compare results, they would surely do this along with using their own mice. The more ways to compare experiments, the more sure we will be about results. I understand cleaning up code is a lot of work, so don't do it, just release it as it is. I know it will be ugly, will include obscenity, etc. If somebody need it, it will do the rest of work.

jonhendry 15y ago
"The more ways to compare experiments, the more sure we will be about results." No. The more exactly you duplicate the original experiment, the more likely you duplicate any confounding issues. If someone observes something through a telescope, it's best to verify it through a different telescope somewhere else, to exclude the possibility of an optical quirk of the first telescope.
- ajuc 15y ago
  Some people will run the same code on the same data. They will get the same results, but so what. Some other people will run the same code on different data (maybe from simulation, or when checking their own theory). They will get some other results, or the same. Some people will recreate experiment from scratch, and get code B and data B. Some people will run code A on data B. Some people will run code B on data A. Now we can't do that. The code is already written, it's waste to hide it, it's not like publishing code prohibit other people from writing their own code. That's how you check for errors - by changing as little as possible and observing results.

JonnieCache 15y ago

>Biology researchers don't get to reuse the other guy's mice In a sense, they actually do. https://secure.wikimedia.org/wikipedia/en/wiki/C57BL/6 https://secure.wikimedia.org/wikipedia/en/wiki/C57BL/6 https://secure.wikimedia.org/wikipedia/en/wiki/BALB/c https://secure.wikimedia.org/wikipedia/en/wiki/BALB/c

jonhendry 15y ago
They use identically-specified mice. They don't use the same mice. The mice used by one lab could, theoretically, be off-spec mutants. Or the lab could have made mixed up which mice they used. Saying you used a particular strain of mouse is like saying you used a particular algorithm on your data. Asking to use the exact individual mice used by another lab might not reveal an error such as mixed-up strains.
- JonnieCache 15y ago
  Sure. I wasn't posting those links to further this argument, I posted them simply because they are interesting. Besides, they're only inbred strains, not clones.
  - jonhendry 15y ago
    They can also be pretty damned expensive. Like $400+ for a mouse.
    - JonnieCache 15y ago
      Looks like I'm in the wrong business. How does that come about? Patent shenanigans?
      - jonhendry 15y ago
        Probably. But really, if you're spending $50,000 on an experiment, you're probably more interested in getting mice that are really what it says on the label, than in saving a few bucks and possibly shooting your experiment and/or career in the nuts. Pretty much anything 'lab grade' is going to be expensive. The lab I worked in ordered a lab grade laser for optogenetics experiments, and that cost something like $18k. Presumably that gets you a very precise, stable wavelength.