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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

#21

Post by chrisseaton »

OldGuyInTheClub wrote: post #20
chrisseaton wrote: post #19

Earlier quoted context omitted.

> 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 publicati…

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

You're listing a lot of reasons why you think it's not worth it!

> Reverse engineering a piece of purchased equipment to publish its BoM now becomes a required part of scientific publication?

No, you mis-read me. I said if it's an existing piece of equipment just say you used that piece of equipment.

Re: Getting a scientific prize for open-source software

#22

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…

@chrisseaton: Can't reply at the correct indentation level but

> You're listing a lot of reasons why you think it's not worth it!

No, I am saying that it is not a new concept. I am all for it and tried to hew to that standard in the papers I've written.

And since I can't reply at the correct level, I'll take that as a hint that the site doesn't really want this and stop here.

Thanks for the discussion.

Re: Getting a scientific prize for open-source software

#23

Post by luthaf »

hobofan wrote: post #15
luthaf wrote: post #13

Earlier quoted context omitted.

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)…

> I found their interfaces especially for simple things (traversing atoms/bonds in a molecule) quite unwieldy.

Somehow the same for me, this is part of why I started my own project (http://chemfiles.org). I have the impression that for cheminformatics you want to see molecules as graphes, is this true or is a list of bonds enough for usual purposes?

I have heard of OEChem but never used it. I'll try to find some documentation to have a look.

Re: Getting a scientific prize for open-source software

#24

Post by dekhn »

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.

I think most people who have worked in science long enough realize that publications are not even minimum-viable: they often omit absolutely necessary information. Sometimes this is intentional, but most of the time, it's just assumed that the reproducer is working in a world-class lab and gets advice/help to implement state-of-the-art work.

Re: Getting a scientific prize for open-source software

#25

Post by hobofan »

luthaf wrote: post #23
hobofan wrote: post #15

Earlier quoted context omitted.

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)…

> I found their interfaces especially for simple things (traversing atoms/bonds in a molecule) quite unwieldy. Somehow the same for me, this is part of why I started my own project ( http://chemfiles.org ). I have the impression that for cheminformatics you want to see molecules as graphes, is this true or is a list of bonds enough for usual purposes? I have heard of OEChem but never used it. I'll try to find some do…

> I have the impression that for cheminformatics you want to see molecules as graphes

Yeah, that was my thinking.

I've also seen your work on lumol, so you seem to be one of the few people working in the field with Rust! I just recently started writing a SMILES parser in Rust[0], as a first step towards an in-memory graph representation of molecules. I have a first rough draft of that locally, though it's very rough and changing a lot, as I have to adjust it weekly as I'm basically learning the required theory at the same time :D

[0]: https://github.com/hobofan/smiles-parser

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