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> fully reproducible methods in chemistry experiments Top-tier open source libraries for cheminformatics (or other natural science -informatics flavours) would

> 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...
    - chrisseaton 7y ago
      Doesn’t that prove my point? I know people post their artefacts. I often review them. Not sure what you’re trying to say?
      - OldGuyInTheClub 7y ago
        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.
        chrisseaton 7y ago
        > 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.
        OldGuyInTheClub 7y ago
        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?
        chrisseaton 7y ago
luthaf 7y ago
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.
- hobofan 7y ago
  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.
  - luthaf 7y ago
    > 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 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.
    - hobofan 7y ago
      > 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 https://github.com/hobofan/smiles-parser

> 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...
  - chrisseaton 7y ago
    Doesn’t that prove my point? I know people post their artefacts. I often review them. Not sure what you’re trying to say?
    - OldGuyInTheClub 7y ago
      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.
      - chrisseaton 7y ago
        > 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.
        OldGuyInTheClub 7y ago
        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?
        chrisseaton 7y ago

luthaf 7y ago

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.

hobofan 7y ago
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.
- luthaf 7y ago
  > 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 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.
  - hobofan 7y ago
    > 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 https://github.com/hobofan/smiles-parser