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biocore / qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
GNU General Public License v2.0
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wrapped software citation concerns raised at stamps #1081

Open wdwvt1 opened 11 years ago

wdwvt1 commented 11 years ago

A concern raised at STAMPS is that the software that QIIME wraps doesn't receive enough citation when that software is used in one of our scripts. Obviously its incumbent upon the researcher to cite their work appropriately, but the concern was that we could make this a lot easier than we do now. There were several suggestions in this regard, the most tractable of which seemed to be:

  1. alter scripts that wrap other tools (and workflows) so that they print information indicating that if you used the script you must cite the additional software it relies on.
  2. create a new script (make_citation.py) that you could enter your command history into, and would return which citations you need to make.
  3. a more prominent listing of this link (http://www.wernerlab.org/software/macqiime/citations) on qiime.org with explanation . This issue was raised by several people, but I unsure of empirical data which suggests this is actually occurring (i.e. I didn't look for papers that cited QIIME but not another tool when it would have been used by default).
lkursell commented 11 years ago

This is more an issue with things like pick_open_reference - it seems that it would be pretty easy to see what options that user past, and then create a citations.txt file whenever the workflow is run?

On Aug 7, 2013, at 9:46 AM, Will Van Treuren notifications@github.com wrote:

A concern raised at STAMPS is that the software that QIIME wraps doesn't receive enough citation when that software is used in one of our scripts. Obviously its incumbent upon the researcher to cite their work appropriately, but the concern was that we could make this a lot easier than we do now. There were several suggestions in this regard, the most tractable of which seemed to be:

  1. alter scripts that wrap other tools (and workflows) so that they print information indicating that if you used the script you must cite the additional software it relies on.
  2. create a new script (make_citation.py) that you could enter your command history into, and would return which citations you need to make.
  3. a more prominent listing of this link (http://www.wernerlab.org/software/macqiime/citations) on qiime.org with explanation . This issue was raised by several people, but I unsure of empirical data which suggests this is actually occurring (i.e. I didn't look for papers that cited QIIME but not another tool when it would have been used by default).

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ElDeveloper commented 11 years ago

@meren just a heads up on this issue.