5 ms·

Getting a scientific prize for open-source software

142 points by gorpovitch 7y ago

bpesquet 7y ago
Some historical context on scikit-learn: https://orbi.uliege.be/bitstream/2268/154357/1/paper.pdf https://orbi.uliege.be/bitstream/2268/154357/1/paper.pdf (2013) https://amueller.github.io/papers/wo_the_machine_varoquaux.pdf https://amueller.github.io/papers/wo_the_machine_varoquaux.p... (2015)
lonelappde 7y ago
OP is right-on as to why this is a big deal in academia. I want to see it spread beyond computer programming libraries into areas where sharing is harder, like open source scientific equipment and fully reproducible methods in chemistry experiments.
- chrisseaton 7y ago
  > OP is right-on as to why this is a big deal in academia. The ACM (academic computer science group) has awarded prizes to these open source systems projects amongst others recently: - Wireshark - Jupyter - GCC - Mach - Coq - LLVM - Eclipse - make - Java - Tcl/Tk The linked article is written like the academy never works on or recognises open source software or implementation work, or using open licences is unusual. That's not true.
  - hobofan 7y ago
    OP was talking about academia in general, and not just about CS-academia, which is of course a lot more sensitive to open source software. In traditional (= non-CS) academia, proprietary software is still very much the norm, and as long as institutes get a free license for academic usage they also don't seem to care about open source too much. I don't know how much precedent there is, but such recognition from traditional academia still seems to be pretty rare and worthy of highlighting.
  - OldGuyInTheClub 7y ago
    Yes. The self-congratulation was very off putting.
- hobofan 7y ago
  > fully reproducible methods in chemistry experiments Top-tier open source libraries for cheminformatics (or other natural science -informatics flavours) would already be a welcome start.
  - OldGuyInTheClub 7y ago
    Published chemical syntheses are described in very great detail. Physical chemistry/spectroscopy papers likewise describe apparatus, collection, and analysis often down to the nuts and bolts. I don't see how to open source work requiring a femtosecond mid-infrared laser or a prep requiring a synthesis lab with all the reagents, labware, and safety equipment. Buried in the open source PR is the unshakeable underlying belief that science begins when the data are in the can and ready for analysis.
    - chrisseaton 7y ago
      > I don't see how to open source work requiring a femtosecond mid-infrared laser or a prep requiring a synthesis lab with all the reagents, labware, and safety equipment. You can put text documents on GitHub describing process, in the same way as you can code and data. If you have some setup with a femtosecond mid-infrared laser or prep requiring a synthesis lab with all the reagents, labware, and safety equipment you can open source the bill of parts, the build instructions and the lab book. It'd probably be very valuable to do that so please do!
      - OldGuyInTheClub 7y ago
        Here are the freely available supplemental data to a paper in the Journal of the American Chemical Society blending organic synthesis, computation, and spectral characterization. 122 pages of exquisite details from a multi-lab collaboration. Lots more like it out there. Note: I am not in any way affiliated with this research or the labs involved. This came out of a quick search. https://pubs.acs.org/doi/suppl/10.1021/jacs.6b13031/suppl_file/ja6b13031_si_001.pdf https://pubs.acs.org/doi/suppl/10.1021/jacs.6b13031/suppl_fi...
fghtr 7y ago
If you think that all software written on public money should be public, consider this petition: https://publiccode.eu https://publiccode.eu
- OrgNet 7y ago
  I think the budget used to make this software possible should also be public... yet we have a black budget

142 points by gorpovitch 7y ago

Some historical context on scikit-learn: https://orbi.uliege.be/bitstream/2268/154357/1/paper.pdf https://orbi.uliege.be/bitstream/2268/154357/1/paper.pdf (2013) https://amueller.github.io/papers/wo_the_machine_varoquaux.pdf https://amueller.github.io/papers/wo_the_machine_varoquaux.p... (2015)

lonelappde 7y ago

OP is right-on as to why this is a big deal in academia. I want to see it spread beyond computer programming libraries into areas where sharing is harder, like open source scientific equipment and fully reproducible methods in chemistry experiments.

chrisseaton 7y ago
> OP is right-on as to why this is a big deal in academia. The ACM (academic computer science group) has awarded prizes to these open source systems projects amongst others recently: - Wireshark - Jupyter - GCC - Mach - Coq - LLVM - Eclipse - make - Java - Tcl/Tk The linked article is written like the academy never works on or recognises open source software or implementation work, or using open licences is unusual. That's not true.
- hobofan 7y ago
  OP was talking about academia in general, and not just about CS-academia, which is of course a lot more sensitive to open source software. In traditional (= non-CS) academia, proprietary software is still very much the norm, and as long as institutes get a free license for academic usage they also don't seem to care about open source too much. I don't know how much precedent there is, but such recognition from traditional academia still seems to be pretty rare and worthy of highlighting.
- OldGuyInTheClub 7y ago
  Yes. The self-congratulation was very off putting.
hobofan 7y ago
> fully reproducible methods in chemistry experiments Top-tier open source libraries for cheminformatics (or other natural science -informatics flavours) would already be a welcome start.
- OldGuyInTheClub 7y ago
  Published chemical syntheses are described in very great detail. Physical chemistry/spectroscopy papers likewise describe apparatus, collection, and analysis often down to the nuts and bolts. I don't see how to open source work requiring a femtosecond mid-infrared laser or a prep requiring a synthesis lab with all the reagents, labware, and safety equipment. Buried in the open source PR is the unshakeable underlying belief that science begins when the data are in the can and ready for analysis.
  - chrisseaton 7y ago
    > I don't see how to open source work requiring a femtosecond mid-infrared laser or a prep requiring a synthesis lab with all the reagents, labware, and safety equipment. You can put text documents on GitHub describing process, in the same way as you can code and data. If you have some setup with a femtosecond mid-infrared laser or prep requiring a synthesis lab with all the reagents, labware, and safety equipment you can open source the bill of parts, the build instructions and the lab book. It'd probably be very valuable to do that so please do!
    - OldGuyInTheClub 7y ago
      Here are the freely available supplemental data to a paper in the Journal of the American Chemical Society blending organic synthesis, computation, and spectral characterization. 122 pages of exquisite details from a multi-lab collaboration. Lots more like it out there. Note: I am not in any way affiliated with this research or the labs involved. This came out of a quick search. https://pubs.acs.org/doi/suppl/10.1021/jacs.6b13031/suppl_file/ja6b13031_si_001.pdf https://pubs.acs.org/doi/suppl/10.1021/jacs.6b13031/suppl_fi...

fghtr 7y ago

If you think that all software written on public money should be public, consider this petition: https://publiccode.eu https://publiccode.eu

OrgNet 7y ago
I think the budget used to make this software possible should also be public... yet we have a black budget