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Getting a scientific prize for open-source software

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Re: Getting a scientific prize for open-source software

#11

Post by chrisseaton »

OldGuyInTheClub wrote: post #10
chrisseaton wrote: post #9

Earlier quoted context omitted.

> 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 yo…

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…

Doesn’t that prove my point? I know people post their artefacts. I often review them. Not sure what you’re trying to say?

Re: Getting a scientific prize for open-source software

#12

Post by OldGuyInTheClub »

chrisseaton wrote: post #11
OldGuyInTheClub wrote: post #10

Earlier quoted context omitted.

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…

Doesn’t that prove my point? I know people post their artefacts. I often review them. Not sure what you’re trying to say?

Reproducing that paper will be very difficult even though all the information is out there. There is a world of science outside of data processing.

Re: Getting a scientific prize for open-source software

#13

Post by luthaf »

hobofan wrote: post #7
lonelappde wrote: post #3

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.

> 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.

What do you think is missing in the current offering (OpenBabel, RDKIT, maybe some other I am missing)?

Context: I do research in computational chemistry, and write an open source library for this, that could be used for cheminformatics too. I don't really know what is needed for this though, since I never touched cheminformatics.

Re: Getting a scientific prize for open-source software

#15

Post by hobofan »

luthaf wrote: post #13
hobofan wrote: post #7

Earlier quoted context omitted.

> 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.

What do you think is missing in the current offering (OpenBabel, RDKIT, maybe some other I am missing)? Context: I do research in computational chemistry, and write an open source library for this, that could be used for cheminformatics too. I don't really know what is needed for this though, since I never touched cheminformatics.

I've dabbled a bit with OpenBabel and RDKIT, but I found their interfaces especially for simple things (traversing atoms/bonds in a molecule) quite unwieldy. I suspect that a big part of this could "just" be missing documentation / tutorials to get into it.

Maybe I'm just not deep enough into it, but from my impression so far especially when it comes to application-level software (in contrast to specialized research), OEChem and similar closed source libraries seem to be the most widely used ones, with nothing quite comparable available.

Context: Software Engineer that is also currently a biochemistry undergraduate.

Re: Getting a scientific prize for open-source software

#16

Post by chrisseaton »

OldGuyInTheClub wrote: post #12
chrisseaton wrote: post #11

Earlier quoted context omitted.

Doesn’t that prove my point? I know people post their artefacts. I often review them. Not sure what you’re trying to say?

Reproducing that paper will be very difficult even though all the information is out there. There is a world of science outside of data processing.

> There is a world of science outside of data processing.

Yes, but that's documented in lab books and procedure documents. Or at least it should be! If it isn't, how are they able to explain their own research? And those can be open sourced.

Re: Getting a scientific prize for open-source software

#18

Post by OldGuyInTheClub »

chrisseaton wrote: post #16
OldGuyInTheClub wrote: post #12

Earlier quoted context omitted.

Reproducing that paper will be very difficult even though all the information is out there. There is a world of science outside of data processing.

> There is a world of science outside of data processing. Yes, but that's documented in lab books and procedure documents. Or at least it should be! If it isn't, how are they able to explain their own research? And those can be open sourced.

The ethos of documenting and describing research in detailed technical publications has been around for a very long time. That supplemental data I referenced has a phenomenal amount of detail and is only one example. They have done as good a job of open sourcing as is possible. Having read other papers from those lab chiefs (Zare, Houk, Baran, Grubbs, Stoltz) I know that they are scrupulous about the detail they publish.

Even so, very few people will be able to replicate that work outside without a very well funded laboratory or collaboration of their own. Lab notebooks contain a vast amount of tangential or irrelevant data which are distilled into the publication. What good is a process document for obtaining an x-ray structure if the diffractometer costs a fortune and is a shared departmental or even national resource? In your example, how deep does the bill of materials go? Is it sufficient to state that one needs a Bruker FTIR or Coherent optical parametric oscillator or do those have to be decomposed into the lowest-level components?

Re: Getting a scientific prize for open-source software

#19

Post by chrisseaton »

OldGuyInTheClub wrote: post #18
chrisseaton wrote: post #16

Earlier quoted context omitted.

> There is a world of science outside of data processing. Yes, but that's documented in lab books and procedure documents. Or at least it should be! If it isn't, how are they able to explain their own research? And those can be open sourced.

The ethos of documenting and describing research in detailed technical publications has been around for a very long time. That supplemental data I referenced has a phenomenal amount of detail and is only one example. They have done as good a job of open sourcing as is possible. Having read other papers from those lab chiefs (Zare, Houk, Baran, Grubbs, Stoltz) I know that they are scrupulous about the detail they publ…

> Even so, very few people will be able to replicate that work outside without a very well funded laboratory or collaboration of their own.

That's not a reason to not be open about it!

> What good is a process document for obtaining an x-ray structure if the diffractometer costs a fortune and is a shared departmental or even national resource?

I think it's inherently good! Even if you think can't use it right now, it's good to put it all out there for people looking and into the archives to keep it for the future.

> In your example, how deep does the bill of materials go?

Well if bills of materials are available for your components themselves then you don't need to break them down yourself.

Re: Getting a scientific prize for open-source software

#20

Post by OldGuyInTheClub »

chrisseaton wrote: post #19
OldGuyInTheClub wrote: post #18

Earlier quoted context omitted.

The ethos of documenting and describing research in detailed technical publications has been around for a very long time. That supplemental data I referenced has a phenomenal amount of detail and is only one example. They have done as good a job of open sourcing as is possible. Having read other papers from those lab chiefs (Zare, Houk, Baran, Grubbs, Stoltz) I know that they are scrupulous about the detail they publ…

> Even so, very few people will be able to replicate that work outside without a very well funded laboratory or collaboration of their own. That's not a reason to not be open about it! > What good is a process document for obtaining an x-ray structure if the diffractometer costs a fortune and is a shared departmental or even national resource? I think it's inherently good! Even if you think can't use it right now, it…

> That's not a reason to not be open about it!

We're talking past each other. Openness in methods has been around in the physical and biological sciences for a very long time.

> Well if bills of materials are available for your components themselves then you don't need to break them down yourself.

Reverse engineering a piece of purchased equipment to publish its BoM now becomes a required part of scientific publication? Or, expecting a manufacturer to provide it and authorize it for general release? I don't think that's realistic.

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