Update: Open Science conclusion; and PNNL NWChem/CML/Quixote update

#oss2011 @okfn


After my talk at OSS I published two posts on the value of Open Access – I used challenging language which has upset several people but seems to find a chord with others. The discussion has taken place on the Open Knowledge Foundation discussion list (http://lists.okfn.org/pipermail/open-science/2011-October/001032.html and about 25 more posts, culminating currently in a very long and researched post (http://lists.okfn.org/pipermail/open-science/2011-October/001053.html ) by Jenny Molloy, my co-presenter at OSS. Further discussion can take place on this list – it’s open to everyone.

For the next few days I am now devoting my energies to helping create the first fully Open Computational chemistry system. This is based on:

  • NWChem http://www.nwchem-sw.org/index.php/Main_Page which last year became fully Open Source. It’s the main Open program for atomistic calculations, and is complemented by Open plane-wave codes such as ABINIT, MPQC and Quantum Espresso (Please comment if I have missed any – I am also not aware of a list of Open Source computational chemistry – not the same as cheminformatics).
  • Chemical Markup Language and specializations in conventions such as CMLComp and compchem.
  • The JumboConverters framework
  • The Blue Obelisk (includes cclib, openbabel, Avogadro, Jmol, etc.) and other Open Source chemistry tools.
  • Chempound (a repository for semantic chemistry) built by Sam Adams.
  • The Quixote community http://quixote.wikispot.org/
  • The FoX library for XML and CML in Fortran

I have blogged about most of these before. At present what we are doing is:

  • Define a top level dictionary for compchem. Bert deJong at PNNL is optimistic that this is feasible in a reasonable time. It will be a community effort.
  • Define a revised convention for compchem (compchem1, say). Bert thinks there is a very clear infrastructure to almost all QC codes and that we can implement this.
  • Add CML output to NWChem. We are halfway there. I have compile FoX on windows and we are currently getting NWChem running on my machine

This will be supported by dictionary validation and document validation.

Anyone interested should post a comment or mail me or the Quixote list – see main page above