Comments on: Can Open Source Work in Chemistry?

By: Geoff

Geoff — Fri, 04 Nov 2005 20:14:39 +0000

Noel, since I’m willing to include molecular mechanics / dynamics codes and DFT codes from physics groups (you include ABINIT), there’s a lot more.
DFT++, Gromacs, YaehMOP, PWSCF, Moscito, Moldy, CAMPOS, MMTK, Spinor, octopus, CP2K, Dacapo, PEtot, Socorro.
(I’m not sure if that’s it. These are codes, where I’ve checked the license.)

There’s actually a pretty good list at FSAtom.org. (I believe this dates from a conference at CECAM.)

There are also several quasi-open source chemistry packages, i.e., free redistribution from the original group, source code available. Perhaps they might move to a more open license, maybe not.

By: Noel O'Boyle

Noel O'Boyle — Fri, 04 Nov 2005 09:38:30 +0000

I am currently counting up the number of open-source computational chemistry packages. My grand total so far is three: PyQuante, MPQC and ABINIT. Can you think of any more?

By: Geoff

Geoff — Wed, 30 Mar 2005 21:36:33 +0000

Peter flatters me. I’m hardly the only contributor to Open Babel — he contributed a large chunk of CML code as well as some other important pieces.

As I remarked to Peter during the ACS conference, I think one advantage of open access is that it’s “sticky.” In the terminology used by Malcolm Gladwell in his book Tipping Point open resources often snowball because it’s hard to reverse the trend. And much like Peter, I don’t think the issue is necessarily finances but access to the data and research. Why cannot the public, educators, or other researchers obtain my data sets for their uses? Sometimes they can, but not always?

In the context of programming and coding (i.e., this post) I think it follows — why can’t I obtain the code or model from a journal to reproduce or build on another research article?

By: Peter Murray-Rust

Peter Murray-Rust — Mon, 28 Mar 2005 21:35:10 +0000

I gave a presentation at the ACS on the values of OpenAccess in chemistry (the idea that publicly funded chemical research should be publicly available). It also extends to Open Source, Open data and Open Standards. See:
http://wwmm.ch.cam.ac.uk/presentations/acs2005/index.html

[You will need SVG (downalod from http://www.adobe.com/svg + IE to see the pictures]

BTW Geoff has done great work in continuing to develop OpenBabel - an important Open chemistry program