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