[gmx-developers] Re: markup for macromolecules in biology

Kaihsu Tai kaihsu at biop.ox.ac.uk
Sun Oct 12 16:56:33 CEST 2003

(copying to the GROMACS developers mailing list as well)

Peter Murray-Rust, 2003-10-12 11:39:58+0100:
> >We are hoping to start a collaboration with the developers
> >of the molecular dynamics simulation package GROMACS
> >"http://www.gromacs.org/".
> Have you contacted them?
> The GROMACS group have contacted me about jointly creating an XML
> representation for GROMACS. We don't have details yet but I would expect
> that it would be able to support your requirements.

Yes, we have contacted the GROMACS developers.  My colleague
Stuart Murdock talked with David van der Spoel at a
conference this week.  Mark Sansom suggested that we have a
'triangle' of collaboration....

> >At the moment BioSimGrid has a relational database as its
> >backend, but so far it appears that a frontend based on some
> >standardized markup language across simulation packages
> >would be helpful in depositing data.  Would you like to
> >further discuss this matter with us, and possibly also the
> >GROMACS developers?
> I would be delighted to talk with you. Basically there is a family of
> markup languages based on CML (Chemical Markup Language). We have tools
> that allow each domain to create their own XML schema. We have languages in
> the area of CMLComp (computational), CMLCM (condensed matter) that would be
> most relevant for your interests. These are not finalised and we are very
> happy to be driven by real problems.
> How should we take this forward - should I come to Oxford - and perhaps
> give a demonstration. Or do you wish to come to Cambridge?

I think the most efficient way to start is for us to read
some of your documents, so we know what to expect.  Would
you please send some pointers?  Thanks.

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